HEADER METAL BINDING PROTEIN 17-APR-01 1IG5 TITLE BOVINE CALBINDIN D9K BINDING MG2+ COMPND MOL_ID: 1; COMPND 2 MOLECULE: VITAMIN D-DEPENDENT CALCIUM-BINDING PROTEIN, INTESTINAL; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: CALBINDIN D9K; COMPND 5 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: BOS TAURUS; SOURCE 3 ORGANISM_COMMON: CATTLE; SOURCE 4 ORGANISM_TAXID: 9913; SOURCE 5 GENE: SYNTHETIC GENE; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 8 EXPRESSION_SYSTEM_STRAIN: MM294; SOURCE 9 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 10 EXPRESSION_SYSTEM_PLASMID: PICB1 KEYWDS CALCIUM-BINDING PROTEIN, EF-HAND, MAGNESIUM BINDING, METAL BINDING KEYWDS 2 PROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR E.M.ANDERSSON,L.A.SVENSSON REVDAT 3 04-OCT-17 1IG5 1 REMARK REVDAT 2 24-FEB-09 1IG5 1 VERSN REVDAT 1 25-APR-01 1IG5 0 SPRSDE 25-APR-01 1IG5 5ICB JRNL AUTH M.ANDERSSON,A.MALMENDAL,S.LINSE,I.IVARSSON,S.FORSEN, JRNL AUTH 2 L.A.SVENSSON JRNL TITL STRUCTURAL BASIS FOR THE NEGATIVE ALLOSTERY BETWEEN CA(2+)- JRNL TITL 2 AND MG(2+)-BINDING IN THE INTRACELLULAR CA(2+)-RECEPTOR JRNL TITL 3 CALBINDIN D9K. JRNL REF PROTEIN SCI. V. 6 1139 1997 JRNL REFN ISSN 0961-8368 JRNL PMID 9194174 REMARK 2 REMARK 2 RESOLUTION. 1.50 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : X-PLOR 3.851 REMARK 3 AUTHORS : BRUNGER REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.50 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 10.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : 2.000 REMARK 3 DATA CUTOFF HIGH (ABS(F)) : 950202.000 REMARK 3 DATA CUTOFF LOW (ABS(F)) : 0.0000 REMARK 3 COMPLETENESS (WORKING+TEST) (%) : 66.3 REMARK 3 NUMBER OF REFLECTIONS : 8452 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 SET) : 0.196 REMARK 3 FREE R VALUE : 0.285 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 10.400 REMARK 3 FREE R VALUE TEST SET COUNT : 882 REMARK 3 ESTIMATED ERROR OF FREE R VALUE : 0.010 REMARK 3 REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN. REMARK 3 TOTAL NUMBER OF BINS USED : 6 REMARK 3 BIN RESOLUTION RANGE HIGH (A) : 1.50 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.59 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 24.00 REMARK 3 REFLECTIONS IN BIN (WORKING SET) : 446 REMARK 3 BIN R VALUE (WORKING SET) : 0.2820 REMARK 3 BIN FREE R VALUE : 0.3370 REMARK 3 BIN FREE R VALUE TEST SET SIZE (%) : 10.40 REMARK 3 BIN FREE R VALUE TEST SET COUNT : 52 REMARK 3 ESTIMATED ERROR OF BIN FREE R VALUE : 0.047 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 596 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 1 REMARK 3 SOLVENT ATOMS : 50 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 22.80 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 25.50 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : NULL REMARK 3 B22 (A**2) : NULL REMARK 3 B33 (A**2) : NULL REMARK 3 B12 (A**2) : NULL REMARK 3 B13 (A**2) : NULL REMARK 3 B23 (A**2) : NULL REMARK 3 REMARK 3 ESTIMATED COORDINATE ERROR. REMARK 3 ESD FROM LUZZATI PLOT (A) : 0.22 REMARK 3 ESD FROM SIGMAA (A) : 0.19 REMARK 3 LOW RESOLUTION CUTOFF (A) : 5.00 REMARK 3 REMARK 3 CROSS-VALIDATED ESTIMATED COORDINATE ERROR. REMARK 3 ESD FROM C-V LUZZATI PLOT (A) : 0.29 REMARK 3 ESD FROM C-V SIGMAA (A) : 0.16 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES. REMARK 3 BOND LENGTHS (A) : 0.020 REMARK 3 BOND ANGLES (DEGREES) : 1.900 REMARK 3 DIHEDRAL ANGLES (DEGREES) : 21.60 REMARK 3 IMPROPER ANGLES (DEGREES) : 1.750 REMARK 3 REMARK 3 ISOTROPIC THERMAL MODEL : RESTRAINED REMARK 3 REMARK 3 ISOTROPIC THERMAL FACTOR RESTRAINTS. RMS SIGMA REMARK 3 MAIN-CHAIN BOND (A**2) : 1.840 ; 1.500 REMARK 3 MAIN-CHAIN ANGLE (A**2) : 2.920 ; 2.000 REMARK 3 SIDE-CHAIN BOND (A**2) : 3.350 ; 2.000 REMARK 3 SIDE-CHAIN ANGLE (A**2) : 5.270 ; 2.500 REMARK 3 REMARK 3 NCS MODEL : NULL REMARK 3 REMARK 3 NCS RESTRAINTS. RMS SIGMA/WEIGHT REMARK 3 GROUP 1 POSITIONAL (A) : NULL ; NULL REMARK 3 GROUP 1 B-FACTOR (A**2) : NULL ; NULL REMARK 3 REMARK 3 PARAMETER FILE 1 : PARHCSDX.PRO REMARK 3 PARAMETER FILE 2 : PARAM19.SOL REMARK 3 PARAMETER FILE 3 : PARAM_MG.ION REMARK 3 PARAMETER FILE 4 : NULL REMARK 3 TOPOLOGY FILE 1 : TOPHCSDX.PRO REMARK 3 TOPOLOGY FILE 2 : TOPH19_MOD.SOL REMARK 3 TOPOLOGY FILE 3 : TOPH19.ION REMARK 3 TOPOLOGY FILE 4 : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 1IG5 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 18-APR-01. REMARK 100 THE DEPOSITION ID IS D_1000013243. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 10-NOV-94 REMARK 200 TEMPERATURE (KELVIN) : 295 REMARK 200 PH : 6.4 REMARK 200 NUMBER OF CRYSTALS USED : 2 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : N REMARK 200 RADIATION SOURCE : ROTATING ANODE REMARK 200 BEAMLINE : NULL REMARK 200 X-RAY GENERATOR MODEL : RIGAKU RU200 REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.5418 REMARK 200 MONOCHROMATOR : SI(111) REMARK 200 OPTICS : COLLIMATOR REMARK 200 REMARK 200 DETECTOR TYPE : AREA DETECTOR REMARK 200 DETECTOR MANUFACTURER : SIEMENS REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : XSCALE REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 11090 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.500 REMARK 200 RESOLUTION RANGE LOW (A) : 22.300 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 0.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 81.0 REMARK 200 DATA REDUNDANCY : 4.900 REMARK 200 R MERGE (I) : 0.07500 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 14.0000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.50 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.70 REMARK 200 COMPLETENESS FOR SHELL (%) : 58.0 REMARK 200 DATA REDUNDANCY IN SHELL : 2.90 REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : 0.21000 REMARK 200 FOR SHELL : NULL REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MULTIPLE ISOMORPHOUS REMARK 200 REPLACEMENT REMARK 200 SOFTWARE USED: MLPHARE REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 43.00 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.16 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 3M AMMONIUM SULPHATE, 100 MM MAGNESIUM REMARK 280 CHLORIDE, PH 6.4, EVAPORATION, TEMPERATURE 298K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 43 21 2 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,-Y,Z+1/2 REMARK 290 3555 -Y+1/2,X+1/2,Z+3/4 REMARK 290 4555 Y+1/2,-X+1/2,Z+1/4 REMARK 290 5555 -X+1/2,Y+1/2,-Z+3/4 REMARK 290 6555 X+1/2,-Y+1/2,-Z+1/4 REMARK 290 7555 Y,X,-Z REMARK 290 8555 -Y,-X,-Z+1/2 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 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 64.73500 REMARK 290 SMTRY1 3 0.000000 -1.000000 0.000000 16.86500 REMARK 290 SMTRY2 3 1.000000 0.000000 0.000000 16.86500 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 97.10250 REMARK 290 SMTRY1 4 0.000000 1.000000 0.000000 16.86500 REMARK 290 SMTRY2 4 -1.000000 0.000000 0.000000 16.86500 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 32.36750 REMARK 290 SMTRY1 5 -1.000000 0.000000 0.000000 16.86500 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 16.86500 REMARK 290 SMTRY3 5 0.000000 0.000000 -1.000000 97.10250 REMARK 290 SMTRY1 6 1.000000 0.000000 0.000000 16.86500 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 16.86500 REMARK 290 SMTRY3 6 0.000000 0.000000 -1.000000 32.36750 REMARK 290 SMTRY1 7 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY2 7 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 8 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY2 8 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 8 0.000000 0.000000 -1.000000 64.73500 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 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: MONOMERIC REMARK 350 APPLY THE FOLLOWING TO CHAINS: A 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 470 REMARK 470 MISSING ATOM REMARK 470 THE FOLLOWING RESIDUES HAVE MISSING ATOMS (M=MODEL NUMBER; REMARK 470 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; REMARK 470 I=INSERTION CODE): REMARK 470 M RES CSSEQI ATOMS REMARK 470 GLU A 51 CG CD OE1 OE2 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 MG A 78 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HOH A 110 O REMARK 620 2 ASN A 56 OD1 93.9 REMARK 620 3 HOH A 112 O 91.6 91.4 REMARK 620 4 ASP A 54 OD1 98.8 84.4 169.0 REMARK 620 5 ASP A 58 OD1 174.6 81.5 85.8 83.5 REMARK 620 6 GLU A 60 O 94.6 171.0 91.5 91.3 90.2 REMARK 620 N 1 2 3 4 5 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: MUM REMARK 800 EVIDENCE_CODE: AUTHOR REMARK 800 SITE_DESCRIPTION: MG BINDING EF-HAND LOOP. REMARK 800 REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MG A 78 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 3ICB RELATED DB: PDB REMARK 900 REFINED STRUCTURE OF VITAMIN D-DEPENDENT CALCIUM-BINDING PROTEIN REMARK 900 FROM BOVINE INTESTINE REMARK 900 RELATED ID: 4ICB RELATED DB: PDB REMARK 900 PROLINE CIS-TRANS ISOMERS IN CALBINDIN D9K OBSERVED BY X-RAY REMARK 900 CRYSTALLOGRAPHY REMARK 900 RELATED ID: 1IGV RELATED DB: PDB REMARK 900 BOVINE CALBINDIN D9K BINDING MN2+ REMARK 900 RELATED ID: 1CLB RELATED DB: PDB REMARK 900 DETERMINATION OF THE SOLUTION STRUCTURE OF APO CALBINDIN D9K BY NMR REMARK 900 SPECTROSCOPY DBREF 1IG5 A 1 75 UNP P02633 S100G_BOVIN 4 78 SEQRES 1 A 75 LYS SER PRO GLU GLU LEU LYS GLY ILE PHE GLU LYS TYR SEQRES 2 A 75 ALA ALA LYS GLU GLY ASP PRO ASN GLN LEU SER LYS GLU SEQRES 3 A 75 GLU LEU LYS LEU LEU LEU GLN THR GLU PHE PRO SER LEU SEQRES 4 A 75 LEU LYS GLY PRO SER THR LEU ASP GLU LEU PHE GLU GLU SEQRES 5 A 75 LEU ASP LYS ASN GLY ASP GLY GLU VAL SER PHE GLU GLU SEQRES 6 A 75 PHE GLN VAL LEU VAL LYS LYS ILE SER GLN HET MG A 78 1 HETNAM MG MAGNESIUM ION FORMUL 2 MG MG 2+ FORMUL 3 HOH *50(H2 O) HELIX 1 1 SER A 2 ALA A 15 1 14 HELIX 2 2 LYS A 25 PHE A 36 1 12 HELIX 3 3 PRO A 37 LYS A 41 5 5 HELIX 4 4 THR A 45 ASP A 54 1 10 HELIX 5 5 SER A 62 SER A 74 1 13 SHEET 1 A 2 LEU A 23 SER A 24 0 SHEET 2 A 2 GLU A 60 VAL A 61 -1 N VAL A 61 O LEU A 23 LINK MG MG A 78 O HOH A 110 1555 1555 1.96 LINK MG MG A 78 OD1 ASN A 56 1555 1555 2.05 LINK MG MG A 78 O HOH A 112 1555 1555 2.10 LINK MG MG A 78 OD1 ASP A 54 1555 1555 2.06 LINK MG MG A 78 OD1 ASP A 58 1555 1555 2.11 LINK MG MG A 78 O GLU A 60 1555 1555 1.99 SITE 1 MUM 4 ASP A 54 ASN A 56 ASP A 58 GLU A 60 SITE 1 AC1 7 ASP A 54 ASN A 56 ASP A 58 GLU A 60 SITE 2 AC1 7 GLN A 75 HOH A 110 HOH A 112 CRYST1 33.730 33.730 129.470 90.00 90.00 90.00 P 43 21 2 8 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 0.029647 0.000000 0.000000 0.00000 SCALE2 0.000000 0.029647 0.000000 0.00000 SCALE3 0.000000 0.000000 0.007724 0.00000