HEADER SUGAR BINDING PROTEIN 15-MAR-12 4E6R TITLE CRYSTAL STRUCTURE OF A CYTOPLASMIC PROTEIN NCK2 (NCK2) FROM HOMO TITLE 2 SAPIENS AT 2.20 A RESOLUTION COMPND MOL_ID: 1; COMPND 2 MOLECULE: CYTOPLASMIC PROTEIN NCK2; COMPND 3 CHAIN: A, B; COMPND 4 FRAGMENT: SH3 2 DOMAIN RESIDUES 114-170; COMPND 5 SYNONYM: GROWTH FACTOR RECEPTOR-BOUND PROTEIN 4, NCK ADAPTOR PROTEIN COMPND 6 2, NCK-2, SH2/SH3 ADAPTOR PROTEIN NCK-BETA; COMPND 7 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 3 ORGANISM_COMMON: HUMAN; SOURCE 4 ORGANISM_TAXID: 9606; SOURCE 5 GENE: BC007195, GRB4, NCK2; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 8 EXPRESSION_SYSTEM_STRAIN: PB1; SOURCE 9 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 10 EXPRESSION_SYSTEM_PLASMID: SPEEDET KEYWDS SH3 DOMAIN, PROTEIN BINDING, STRUCTURAL GENOMICS, JOINT CENTER FOR KEYWDS 2 STRUCTURAL GENOMICS, JCSG, PROTEIN STRUCTURE INITIATIVE, PSI- KEYWDS 3 BIOLOGY, SUGAR BINDING PROTEIN, PARTNERSHIP FOR T-CELL BIOLOGY, KEYWDS 4 TCELL EXPDTA X-RAY DIFFRACTION AUTHOR JOINT CENTER FOR STRUCTURAL GENOMICS (JCSG),PARTNERSHIP FOR T-CELL AUTHOR 2 BIOLOGY (TCELL) REVDAT 4 01-FEB-23 4E6R 1 REMARK SEQADV LINK REVDAT 3 15-NOV-17 4E6R 1 REMARK REVDAT 2 21-OCT-15 4E6R 1 AUTHOR JRNL REVDAT 1 04-APR-12 4E6R 0 JRNL AUTH JOINT CENTER FOR STRUCTURAL GENOMICS (JCSG), JRNL AUTH 2 PARTNERSHIP FOR T-CELL BIOLOGY (TCELL) JRNL TITL CRYSTAL STRUCTURE OF A CYTOPLASMIC PROTEIN NCK2 (NCK2) FROM JRNL TITL 2 HOMO SAPIENS AT 2.20 A RESOLUTION JRNL REF TO BE PUBLISHED JRNL REFN REMARK 2 REMARK 2 RESOLUTION. 2.20 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.6.0117 REMARK 3 AUTHORS : MURSHUDOV,SKUBAK,LEBEDEV,PANNU,STEINER, REMARK 3 : NICHOLLS,WINN,LONG,VAGIN REMARK 3 REMARK 3 REFINEMENT TARGET : MAXIMUM LIKELIHOOD WITH PHASES REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.20 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 28.86 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.8 REMARK 3 NUMBER OF REFLECTIONS : 12456 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 CROSS-VALIDATION METHOD : THROUGHOUT REMARK 3 FREE R VALUE TEST SET SELECTION : RANDOM REMARK 3 R VALUE (WORKING + TEST SET) : 0.202 REMARK 3 R VALUE (WORKING SET) : 0.201 REMARK 3 FREE R VALUE : 0.227 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.800 REMARK 3 FREE R VALUE TEST SET COUNT : 599 REMARK 3 REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN. REMARK 3 TOTAL NUMBER OF BINS USED : 20 REMARK 3 BIN RESOLUTION RANGE HIGH (A) : 2.20 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.26 REMARK 3 REFLECTION IN BIN (WORKING SET) : 746 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 100.0 REMARK 3 BIN R VALUE (WORKING SET) : 0.2850 REMARK 3 BIN FREE R VALUE SET COUNT : 40 REMARK 3 BIN FREE R VALUE : 0.2820 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 952 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 33 REMARK 3 SOLVENT ATOMS : 33 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 40.20 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 58.24 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 2.58000 REMARK 3 B22 (A**2) : 2.58000 REMARK 3 B33 (A**2) : -3.87000 REMARK 3 B12 (A**2) : 1.29000 REMARK 3 B13 (A**2) : 0.00000 REMARK 3 B23 (A**2) : 0.00000 REMARK 3 REMARK 3 ESTIMATED OVERALL COORDINATE ERROR. REMARK 3 ESU BASED ON R VALUE (A): 0.165 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.150 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.125 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 9.612 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.950 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.940 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 1007 ; 0.015 ; 0.020 REMARK 3 BOND LENGTHS OTHERS (A): 686 ; 0.001 ; 0.020 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 1367 ; 1.769 ; 1.977 REMARK 3 BOND ANGLES OTHERS (DEGREES): 1647 ; 3.916 ; 3.000 REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 120 ; 6.176 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 49 ;33.590 ;23.673 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 131 ;13.602 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 6 ;21.204 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 141 ; 0.091 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 1124 ; 0.006 ; 0.020 REMARK 3 GENERAL PLANES OTHERS (A): 242 ; 0.001 ; 0.020 REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED CONTACTS OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION OTHERS (A): NULL ; NULL ; NULL REMARK 3 H-BOND (X...Y) REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 H-BOND (X...Y) OTHERS (A): NULL ; NULL ; NULL REMARK 3 POTENTIAL METAL-ION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 POTENTIAL METAL-ION OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY VDW REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY VDW OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY H-BOND REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY H-BOND OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY METAL-ION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY METAL-ION OTHERS (A): NULL ; NULL ; NULL REMARK 3 REMARK 3 ISOTROPIC THERMAL FACTOR RESTRAINTS. COUNT RMS WEIGHT REMARK 3 MAIN-CHAIN BOND REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 LONG RANGE B REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 LONG RANGE B OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 REMARK 3 ANISOTROPIC THERMAL FACTOR RESTRAINTS. COUNT RMS WEIGHT REMARK 3 RIGID-BOND RESTRAINTS (A**2): NULL ; NULL ; NULL REMARK 3 SPHERICITY; FREE ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SPHERICITY; BONDED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 REMARK 3 NCS RESTRAINTS STATISTICS REMARK 3 NUMBER OF DIFFERENT NCS GROUPS : 2 REMARK 3 REMARK 3 NCS GROUP NUMBER : 1 REMARK 3 CHAIN NAMES : A B REMARK 3 NUMBER OF COMPONENTS NCS GROUP : 1 REMARK 3 COMPONENT C SSSEQI TO C SSSEQI CODE REMARK 3 1 A 0 A 170 6 REMARK 3 1 B 0 B 170 6 REMARK 3 GROUP CHAIN COUNT RMS WEIGHT REMARK 3 LOOSE POSITIONAL 1 A (A): 797 ; 0.550 ; 5.000 REMARK 3 LOOSE THERMAL 1 A (A**2): 797 ; 5.790 ;10.000 REMARK 3 REMARK 3 NCS GROUP NUMBER : 2 REMARK 3 CHAIN NAMES : A B REMARK 3 NUMBER OF COMPONENTS NCS GROUP : 1 REMARK 3 COMPONENT C SSSEQI TO C SSSEQI CODE REMARK 3 1 B 201 B 500 6 REMARK 3 1 A 206 A 500 6 REMARK 3 GROUP CHAIN COUNT RMS WEIGHT REMARK 3 LOOSE POSITIONAL 2 A (A): 9 ; 0.400 ; 5.000 REMARK 3 LOOSE THERMAL 2 A (A**2): 9 ; 4.700 ;10.000 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : 2 REMARK 3 REMARK 3 TLS GROUP : 1 REMARK 3 NUMBER OF COMPONENTS GROUP : 1 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : A 0 A 170 REMARK 3 ORIGIN FOR THE GROUP (A): -17.2190 88.7200 8.9070 REMARK 3 T TENSOR REMARK 3 T11: 0.2915 T22: 0.0299 REMARK 3 T33: 0.6301 T12: 0.0535 REMARK 3 T13: 0.0832 T23: 0.0476 REMARK 3 L TENSOR REMARK 3 L11: 2.7965 L22: 6.3993 REMARK 3 L33: 4.9210 L12: -0.4566 REMARK 3 L13: 0.2837 L23: -0.6364 REMARK 3 S TENSOR REMARK 3 S11: -0.0293 S12: -0.1463 S13: 0.2006 REMARK 3 S21: 0.8685 S22: 0.0547 S23: 0.1527 REMARK 3 S31: -0.4138 S32: 0.0572 S33: -0.0254 REMARK 3 REMARK 3 TLS GROUP : 2 REMARK 3 NUMBER OF COMPONENTS GROUP : 1 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : B 0 B 170 REMARK 3 ORIGIN FOR THE GROUP (A): -11.4530 65.1500 19.5910 REMARK 3 T TENSOR REMARK 3 T11: 0.0625 T22: 0.0910 REMARK 3 T33: 0.4596 T12: 0.0046 REMARK 3 T13: -0.0016 T23: 0.0514 REMARK 3 L TENSOR REMARK 3 L11: 5.9171 L22: 3.4780 REMARK 3 L33: 3.3245 L12: 0.1863 REMARK 3 L13: 1.2412 L23: -0.2515 REMARK 3 S TENSOR REMARK 3 S11: 0.0996 S12: -0.6244 S13: -0.1871 REMARK 3 S21: 0.4396 S22: 0.0762 S23: 0.2243 REMARK 3 S31: -0.1036 S32: -0.3075 S33: -0.1758 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : BABINET MODEL WITH MASK REMARK 3 PARAMETERS FOR MASK CALCULATION REMARK 3 VDW PROBE RADIUS : 1.20 REMARK 3 ION PROBE RADIUS : 0.80 REMARK 3 SHRINKAGE RADIUS : 0.80 REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: 1. HYDROGENS HAVE BEEN ADDED IN THE REMARK 3 RIDING POSITIONS. 2. ATOM RECORD CONTAINS SUM OF TLS AND REMARK 3 RESIDUAL B FACTORS. 3. ANISOU RECORD CONTAINS SUM OF TLS AND REMARK 3 RESIDUAL U FACTORS. 4. WATERS WERE EXCLUDED FROM AUTOMATIC TLS REMARK 3 ASSIGNMENT. 5. A MET-INHIBITION PROTOCOL WAS USED FOR REMARK 3 SELENOMETHIONINE INCORPORATION DURING PROTEIN EXPRESSION. THE REMARK 3 OCCUPANCY OF THE SE ATOMS IN THE MSE RESIDUES WAS REDUCED TO REMARK 3 0.75 FOR THE REDUCED SCATTERING POWER DUE TO PARTIAL S-MET REMARK 3 INCORPORATION. 6. X-RAY FLUORESCENCE EXCITATION AND WAVELENGTH REMARK 3 SCANS, ANOMALOUS DIFFERENCE FOURIERS AND ITS PRESENCE IN REMARK 3 CRYSTALLIZATION SOLUTION SUPPORT THE MODELING OF ZINC (ZN) IONS. REMARK 3 7. LYSINE RESIDUES WERE METHYLATED PRIOR TO CRYSTALLIZATION AND REMARK 3 ARE MODELED AS DIMETHYL-LYSINE (MLY). THE N-TERMINAL GLYCINE REMARK 3 RESIDUES WERE ALSO METHYLATED IN THIS PROCEDURE AND ARE MODELED REMARK 3 AS N,N-DIMETHYLGLYCINE (DMG). 8. IMIDAZOLE (IMD) FROM THE REMARK 3 CRYSTALLIZATION CONDITION HAS BEEN MODELED. 9. AN UNKNOWN LIGAND REMARK 3 (UNL) HAS BEEN MODELED IN EACH CHAIN. REMARK 4 REMARK 4 4E6R COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 22-MAR-12. REMARK 100 THE DEPOSITION ID IS D_1000071239. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 12-JAN-12 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 8.0 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : SSRL REMARK 200 BEAMLINE : BL9-2 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.91837,0.97949,0.97929 REMARK 200 MONOCHROMATOR : DOUBLE CRYSTAL REMARK 200 OPTICS : DOUBLE CRYSTAL MONOCHROMATOR REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : MARMOSAIC 325 MM CCD REMARK 200 INTENSITY-INTEGRATION SOFTWARE : MOSFLM REMARK 200 DATA SCALING SOFTWARE : SCALA 3.3.20 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 12480 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.200 REMARK 200 RESOLUTION RANGE LOW (A) : 28.862 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 100.0 REMARK 200 DATA REDUNDANCY : 14.00 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : 0.20000 REMARK 200 FOR THE DATA SET : 11.4000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.20 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.26 REMARK 200 COMPLETENESS FOR SHELL (%) : 100.0 REMARK 200 DATA REDUNDANCY IN SHELL : 14.40 REMARK 200 R MERGE FOR SHELL (I) : 0.02100 REMARK 200 R SYM FOR SHELL (I) : 2.06900 REMARK 200 FOR SHELL : 0.300 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: MAD REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MAD REMARK 200 SOFTWARE USED: SHELX, SHARP, SHELXD REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 71.16 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 4.27 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 40.00% POLYETHYLENE GLYCOL 300, 0.20M REMARK 280 ZINC ACETATE, 0.1M IMIDAZOLE PH 8.0, NANODROP, VAPOR DIFFUSION, REMARK 280 SITTING DROP, TEMPERATURE 277K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 65 2 2 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -Y,X-Y,Z+2/3 REMARK 290 3555 -X+Y,-X,Z+1/3 REMARK 290 4555 -X,-Y,Z+1/2 REMARK 290 5555 Y,-X+Y,Z+1/6 REMARK 290 6555 X-Y,X,Z+5/6 REMARK 290 7555 Y,X,-Z+2/3 REMARK 290 8555 X-Y,-Y,-Z REMARK 290 9555 -X,-X+Y,-Z+1/3 REMARK 290 10555 -Y,-X,-Z+1/6 REMARK 290 11555 -X+Y,Y,-Z+1/2 REMARK 290 12555 X,X-Y,-Z+5/6 REMARK 290 REMARK 290 WHERE NNN -> OPERATOR NUMBER REMARK 290 MMM -> TRANSLATION VECTOR REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY TRANSFORMATIONS REMARK 290 THE FOLLOWING TRANSFORMATIONS OPERATE ON THE ATOM/HETATM REMARK 290 RECORDS IN THIS ENTRY TO PRODUCE CRYSTALLOGRAPHICALLY REMARK 290 RELATED MOLECULES. REMARK 290 SMTRY1 1 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 1 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 1 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 2 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 2 0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 45.46600 REMARK 290 SMTRY1 3 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 3 -0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 22.73300 REMARK 290 SMTRY1 4 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 34.09950 REMARK 290 SMTRY1 5 0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 5 -0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 5 0.000000 0.000000 1.000000 11.36650 REMARK 290 SMTRY1 6 0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 6 0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 6 0.000000 0.000000 1.000000 56.83250 REMARK 290 SMTRY1 7 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 7 0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 45.46600 REMARK 290 SMTRY1 8 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 8 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 8 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 9 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 9 -0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 9 0.000000 0.000000 -1.000000 22.73300 REMARK 290 SMTRY1 10 0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 10 -0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 10 0.000000 0.000000 -1.000000 11.36650 REMARK 290 SMTRY1 11 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 11 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 11 0.000000 0.000000 -1.000000 34.09950 REMARK 290 SMTRY1 12 0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 12 0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 12 0.000000 0.000000 -1.000000 56.83250 REMARK 290 REMARK 290 REMARK: NULL REMARK 300 REMARK 300 BIOMOLECULE: 1 REMARK 300 SEE REMARK 350 FOR THE AUTHOR PROVIDED AND/OR PROGRAM REMARK 300 GENERATED ASSEMBLY INFORMATION FOR THE STRUCTURE IN REMARK 300 THIS ENTRY. THE REMARK MAY ALSO PROVIDE INFORMATION ON REMARK 300 BURIED SURFACE AREA. REMARK 300 REMARK: CRYSTAL PACKING ANALYSIS SUGGESTS THE ASSIGNMENT OF A REMARK 300 TETRAMER AS THE SIGNIFICANT OLIGOMERIZATION STATE. REMARK 350 REMARK 350 COORDINATES FOR A COMPLETE MULTIMER REPRESENTING THE KNOWN REMARK 350 BIOLOGICALLY SIGNIFICANT OLIGOMERIZATION STATE OF THE REMARK 350 MOLECULE CAN BE GENERATED BY APPLYING BIOMT TRANSFORMATIONS REMARK 350 GIVEN BELOW. BOTH NON-CRYSTALLOGRAPHIC AND REMARK 350 CRYSTALLOGRAPHIC OPERATIONS ARE GIVEN. REMARK 350 REMARK 350 BIOMOLECULE: 1 REMARK 350 AUTHOR DETERMINED BIOLOGICAL UNIT: TETRAMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: TETRAMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 4500 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 14050 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -270.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, B REMARK 350 BIOMT1 1 1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT2 1 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT3 1 0.000000 0.000000 1.000000 0.00000 REMARK 350 BIOMT1 2 0.500000 -0.866025 0.000000 54.19900 REMARK 350 BIOMT2 2 -0.866025 -0.500000 0.000000 93.87542 REMARK 350 BIOMT3 2 0.000000 0.000000 -1.000000 11.36650 REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CLOSE CONTACTS IN SAME ASYMMETRIC UNIT REMARK 500 REMARK 500 THE FOLLOWING ATOMS ARE IN CLOSE CONTACT. REMARK 500 REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI DISTANCE REMARK 500 OD2 ASP A 128 O3 UNL A 206 2.14 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CLOSE CONTACTS REMARK 500 REMARK 500 THE FOLLOWING ATOMS THAT ARE RELATED BY CRYSTALLOGRAPHIC REMARK 500 SYMMETRY ARE IN CLOSE CONTACT. AN ATOM LOCATED WITHIN 0.15 REMARK 500 ANGSTROMS OF A SYMMETRY RELATED ATOM IS ASSUMED TO BE ON A REMARK 500 SPECIAL POSITION AND IS, THEREFORE, LISTED IN REMARK 375 REMARK 500 INSTEAD OF REMARK 500. ATOMS WITH NON-BLANK ALTERNATE REMARK 500 LOCATION INDICATORS ARE NOT INCLUDED IN THE CALCULATIONS. REMARK 500 REMARK 500 DISTANCE CUTOFF: REMARK 500 2.2 ANGSTROMS FOR CONTACTS NOT INVOLVING HYDROGEN ATOMS REMARK 500 1.6 ANGSTROMS FOR CONTACTS INVOLVING HYDROGEN ATOMS REMARK 500 REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI SSYMOP DISTANCE REMARK 500 O3 UNL B 201 O3 UNL B 201 10665 1.75 REMARK 500 SG CYS A 144 OE2 GLU B 142 10665 2.13 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: COVALENT BOND LENGTHS REMARK 500 REMARK 500 THE STEREOCHEMICAL PARAMETERS OF THE FOLLOWING RESIDUES REMARK 500 HAVE VALUES WHICH DEVIATE FROM EXPECTED VALUES BY MORE REMARK 500 THAN 6*RMSD (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 500 IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 STANDARD TABLE: REMARK 500 FORMAT: (10X,I3,1X,2(A3,1X,A1,I4,A1,1X,A4,3X),1X,F6.3) REMARK 500 REMARK 500 EXPECTED VALUES PROTEIN: ENGH AND HUBER, 1999 REMARK 500 EXPECTED VALUES NUCLEIC ACID: CLOWNEY ET AL 1996 REMARK 500 REMARK 500 M RES CSSEQI ATM1 RES CSSEQI ATM2 DEVIATION REMARK 500 TRP A 159 CE2 TRP A 159 CD2 0.074 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: COVALENT BOND ANGLES REMARK 500 REMARK 500 THE STEREOCHEMICAL PARAMETERS OF THE FOLLOWING RESIDUES REMARK 500 HAVE VALUES WHICH DEVIATE FROM EXPECTED VALUES BY MORE REMARK 500 THAN 6*RMSD (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 500 IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 STANDARD TABLE: REMARK 500 FORMAT: (10X,I3,1X,A3,1X,A1,I4,A1,3(1X,A4,2X),12X,F5.1) REMARK 500 REMARK 500 EXPECTED VALUES PROTEIN: ENGH AND HUBER, 1999 REMARK 500 EXPECTED VALUES NUCLEIC ACID: CLOWNEY ET AL 1996 REMARK 500 REMARK 500 M RES CSSEQI ATM1 ATM2 ATM3 REMARK 500 ASP A 146 CB - CG - OD1 ANGL. DEV. = 6.2 DEGREES REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: TORSION ANGLES REMARK 500 REMARK 500 TORSION ANGLES OUTSIDE THE EXPECTED RAMACHANDRAN REGIONS: REMARK 500 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 500 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 STANDARD TABLE: REMARK 500 FORMAT:(10X,I3,1X,A3,1X,A1,I4,A1,4X,F7.2,3X,F7.2) REMARK 500 REMARK 500 EXPECTED VALUES: GJ KLEYWEGT AND TA JONES (1996). PHI/PSI- REMARK 500 CHOLOGY: RAMACHANDRAN REVISITED. STRUCTURE 4, 1395 - 1400 REMARK 500 REMARK 500 M RES CSSEQI PSI PHI REMARK 500 VAL B 169 49.58 -144.40 REMARK 500 REMARK 500 REMARK: NULL REMARK 620 REMARK 620 METAL COORDINATION REMARK 620 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 620 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE): REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 ZN A 202 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 GLU A 125 OE1 REMARK 620 2 HOH A 709 O 101.4 REMARK 620 N 1 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 ZN A 205 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 GLU A 127 OE1 REMARK 620 2 IMD A 207 N3 122.7 REMARK 620 3 GLU B 142 OE2 147.5 84.6 REMARK 620 4 GLU B 142 OE1 89.7 133.1 57.8 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 ZN A 201 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 GLU A 142 OE2 REMARK 620 2 GLU A 142 OE1 58.5 REMARK 620 3 IMD A 204 N3 82.2 130.7 REMARK 620 4 GLU B 127 OE1 134.7 76.3 132.8 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 ZN B 202 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 GLU B 125 OE2 REMARK 620 2 GLU B 125 OE1 53.1 REMARK 620 3 HOH B 303 O 74.7 124.4 REMARK 620 4 HOH B 319 O 124.5 75.6 159.9 REMARK 620 5 HOH B 320 O 88.8 99.9 96.3 79.6 REMARK 620 N 1 2 3 4 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ZN A 201 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ZN A 202 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ZN A 203 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE IMD A 204 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ZN A 205 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE IMD A 207 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC7 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ZN B 202 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: JCSG-422527 RELATED DB: TARGETTRACK REMARK 999 REMARK 999 SEQUENCE REMARK 999 1. THIS CONSTRUCT WAS EXPRESSED WITH A PURIFICATION TAG REMARK 999 MGSDKIHHHHHHENLYFQG. THE TAG WAS REMOVED WITH TEV PROTEASE LEAVING REMARK 999 ONLY A GLYCINE (0) FOLLOWED BY RESIDUES 114-170 OF THE TARGET REMARK 999 SEQUENCE. 2. THE PROTEIN WAS REDUCTIVELY METHYLATED PRIOR TO REMARK 999 CRYSTALLIZATION. DBREF 4E6R A 114 170 UNP O43639 NCK2_HUMAN 114 170 DBREF 4E6R B 114 170 UNP O43639 NCK2_HUMAN 114 170 SEQADV 4E6R DMG A 0 UNP O43639 EXPRESSION TAG SEQADV 4E6R DMG B 0 UNP O43639 EXPRESSION TAG SEQRES 1 A 58 DMG ILE PRO ALA PHE VAL MLY PHE ALA TYR VAL ALA GLU SEQRES 2 A 58 ARG GLU ASP GLU LEU SER LEU VAL MLY GLY SER ARG VAL SEQRES 3 A 58 THR VAL MSE GLU MLY CYS SER ASP GLY TRP TRP ARG GLY SEQRES 4 A 58 SER TYR ASN GLY GLN ILE GLY TRP PHE PRO SER ASN TYR SEQRES 5 A 58 VAL LEU GLU GLU VAL ASP SEQRES 1 B 58 DMG ILE PRO ALA PHE VAL MLY PHE ALA TYR VAL ALA GLU SEQRES 2 B 58 ARG GLU ASP GLU LEU SER LEU VAL MLY GLY SER ARG VAL SEQRES 3 B 58 THR VAL MSE GLU MLY CYS SER ASP GLY TRP TRP ARG GLY SEQRES 4 B 58 SER TYR ASN GLY GLN ILE GLY TRP PHE PRO SER ASN TYR SEQRES 5 B 58 VAL LEU GLU GLU VAL ASP MODRES 4E6R MLY A 119 LYS N-DIMETHYL-LYSINE MODRES 4E6R MLY A 134 LYS N-DIMETHYL-LYSINE MODRES 4E6R MSE A 141 MET SELENOMETHIONINE MODRES 4E6R MLY A 143 LYS N-DIMETHYL-LYSINE MODRES 4E6R MLY B 119 LYS N-DIMETHYL-LYSINE MODRES 4E6R MLY B 134 LYS N-DIMETHYL-LYSINE MODRES 4E6R MSE B 141 MET SELENOMETHIONINE MODRES 4E6R MLY B 143 LYS N-DIMETHYL-LYSINE HET DMG A 0 6 HET MLY A 119 11 HET MLY A 134 11 HET MSE A 141 8 HET MLY A 143 11 HET DMG B 0 6 HET MLY B 119 11 HET MLY B 134 11 HET MSE B 141 8 HET MLY B 143 11 HET ZN A 201 1 HET ZN A 202 1 HET ZN A 203 1 HET IMD A 204 5 HET ZN A 205 1 HET UNL A 206 9 HET IMD A 207 5 HET UNL B 201 9 HET ZN B 202 1 HETNAM DMG N,N-DIMETHYLGLYCINE HETNAM MLY N-DIMETHYL-LYSINE HETNAM MSE SELENOMETHIONINE HETNAM ZN ZINC ION HETNAM IMD IMIDAZOLE HETNAM UNL UNKNOWN LIGAND HETSYN DMG DIMETHYLGLYCINE FORMUL 1 DMG 2(C4 H9 N O2) FORMUL 1 MLY 6(C8 H18 N2 O2) FORMUL 1 MSE 2(C5 H11 N O2 SE) FORMUL 3 ZN 5(ZN 2+) FORMUL 6 IMD 2(C3 H5 N2 1+) FORMUL 12 HOH *33(H2 O) SHEET 1 A 5 GLN A 156 PRO A 161 0 SHEET 2 A 5 TRP A 148 TYR A 153 -1 N TRP A 149 O PHE A 160 SHEET 3 A 5 ARG A 137 MLY A 143 -1 N MSE A 141 O ARG A 150 SHEET 4 A 5 ILE A 114 VAL A 118 -1 N ILE A 114 O VAL A 140 SHEET 5 A 5 VAL A 165 GLU A 167 -1 O LEU A 166 N PHE A 117 SHEET 1 B 5 GLN B 156 PRO B 161 0 SHEET 2 B 5 TRP B 148 TYR B 153 -1 N GLY B 151 O GLY B 158 SHEET 3 B 5 ARG B 137 MLY B 143 -1 N MSE B 141 O ARG B 150 SHEET 4 B 5 ILE B 114 VAL B 118 -1 N ILE B 114 O VAL B 140 SHEET 5 B 5 VAL B 165 GLU B 167 -1 O LEU B 166 N PHE B 117 SSBOND 1 CYS A 144 CYS B 144 1555 10665 2.02 LINK C VAL A 118 N MLY A 119 1555 1555 1.34 LINK C MLY A 119 N PHE A 120 1555 1555 1.34 LINK C VAL A 133 N MLY A 134 1555 1555 1.33 LINK C MLY A 134 N GLY A 135 1555 1555 1.34 LINK C VAL A 140 N MSE A 141 1555 1555 1.33 LINK C MSE A 141 N GLU A 142 1555 1555 1.33 LINK C GLU A 142 N MLY A 143 1555 1555 1.34 LINK C MLY A 143 N CYS A 144 1555 1555 1.34 LINK C VAL B 118 N MLY B 119 1555 1555 1.34 LINK C MLY B 119 N PHE B 120 1555 1555 1.33 LINK C VAL B 133 N MLY B 134 1555 1555 1.34 LINK C MLY B 134 N GLY B 135 1555 1555 1.33 LINK C VAL B 140 N MSE B 141 1555 1555 1.32 LINK C MSE B 141 N GLU B 142 1555 1555 1.33 LINK C GLU B 142 N MLY B 143 1555 1555 1.33 LINK C MLY B 143 N CYS B 144 1555 1555 1.34 LINK OE1 GLU A 125 ZN ZN A 202 1555 1555 2.51 LINK OE1 GLU A 127 ZN ZN A 205 1555 1555 2.45 LINK OE2 GLU A 142 ZN ZN A 201 1555 1555 1.83 LINK OE1 GLU A 142 ZN ZN A 201 1555 1555 2.65 LINK OD1 ASP A 170 ZN ZN A 203 1555 1555 2.45 LINK ZN ZN A 201 N3 IMD A 204 1555 1555 2.21 LINK ZN ZN A 201 OE1 GLU B 127 1555 1555 2.16 LINK ZN ZN A 202 O HOH A 709 1555 1555 1.88 LINK ZN ZN A 205 N3 IMD A 207 1555 1555 2.04 LINK ZN ZN A 205 OE2 GLU B 142 1555 1555 1.94 LINK ZN ZN A 205 OE1 GLU B 142 1555 1555 2.61 LINK OE2 GLU B 125 ZN ZN B 202 1555 1555 2.50 LINK OE1 GLU B 125 ZN ZN B 202 1555 1555 2.55 LINK ZN ZN B 202 O HOH B 303 1555 1555 1.96 LINK ZN ZN B 202 O HOH B 319 1555 1555 2.60 LINK ZN ZN B 202 O HOH B 320 1555 1555 2.27 SITE 1 AC1 4 GLU A 142 IMD A 204 GLU B 127 ASP B 146 SITE 1 AC2 4 GLU A 125 HOH A 708 HOH A 709 HOH A 711 SITE 1 AC3 3 GLU A 168 ASP A 170 MLY B 143 SITE 1 AC4 6 GLU A 142 ZN A 201 GLU B 127 CYS B 144 SITE 2 AC4 6 ASP B 146 TRP B 159 SITE 1 AC5 5 GLU A 127 CYS A 144 ASP A 146 IMD A 207 SITE 2 AC5 5 GLU B 142 SITE 1 AC6 6 GLU A 127 CYS A 144 ASP A 146 TRP A 159 SITE 2 AC6 6 ZN A 205 GLU B 142 SITE 1 AC7 5 GLU B 125 HOH B 302 HOH B 303 HOH B 319 SITE 2 AC7 5 HOH B 320 CRYST1 108.398 108.398 68.199 90.00 90.00 120.00 P 65 2 2 24 ORIGX1 1.000000 0.000000 0.000000 0.00000 ORIGX2 0.000000 1.000000 0.000000 0.00000 ORIGX3 0.000000 0.000000 1.000000 0.00000 SCALE1 0.009225 0.005326 0.000000 0.00000 SCALE2 0.000000 0.010652 0.000000 0.00000 SCALE3 0.000000 0.000000 0.014663 0.00000