HEADER TRANSCRIPTION 12-DEC-01 1KLS TITLE NMR STRUCTURE OF THE ZFY-6T[Y10L] ZINC FINGER COMPND MOL_ID: 1; COMPND 2 MOLECULE: ZINC FINGER Y-CHROMOSOMAL PROTEIN; COMPND 3 CHAIN: A; COMPND 4 ENGINEERED: YES; COMPND 5 MUTATION: YES SOURCE MOL_ID: 1; SOURCE 2 SYNTHETIC: YES; SOURCE 3 OTHER_DETAILS: THIS PEPTIDE WAS SYNTHESIZED BY SOLID-PHASE SOURCE 4 SYNTHESIS. THE SEQUENCE OF THE PEPTIDE IS NATURALLY FOUND IN HOMO SOURCE 5 SAPIENS (HUMAN). KEYWDS ZINC FINGER, TRANSCRIPTION EXPDTA SOLUTION NMR NUMMDL 30 AUTHOR M.J.LACHENMANN,J.E.LADBURY,N.B.PHILLIPS,N.NARAYANA,X.QIAN,M.A.WEISS REVDAT 3 27-OCT-21 1KLS 1 REMARK SEQADV LINK REVDAT 2 24-FEB-09 1KLS 1 VERSN REVDAT 1 13-MAR-02 1KLS 0 JRNL AUTH M.J.LACHENMANN,J.E.LADBURY,N.B.PHILLIPS,N.NARAYANA,X.QIAN, JRNL AUTH 2 M.A.WEISS JRNL TITL THE HIDDEN THERMODYNAMICS OF A ZINC FINGER. JRNL REF J.MOL.BIOL. V. 316 969 2002 JRNL REFN ISSN 0022-2836 JRNL PMID 11884136 JRNL DOI 10.1006/JMBI.2001.5335 REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : VNMR 4.3, 5.3, X-PLOR 3.1 REMARK 3 AUTHORS : VARIAN, INC. (VNMR), BRUNGER, A.T. (X-PLOR) REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: STRUCTURES ARE BASED ON 265 REMARK 3 INTERRESIDUE NOE-DERIVED DISTANCE CONSTRAINTS, 27 DIHEDRAL ANGLE REMARK 3 RESTRAINTS, AND 10 HYDROGEN BOND RESTRAINTS. REMARK 4 REMARK 4 1KLS COMPLIES WITH FORMAT V. 3.15, 01-DEC-08 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 14-DEC-01. REMARK 100 THE DEPOSITION ID IS D_1000015087. REMARK 210 REMARK 210 EXPERIMENTAL DETAILS REMARK 210 EXPERIMENT TYPE : NMR REMARK 210 TEMPERATURE (KELVIN) : 298; 298 REMARK 210 PH : 6.0; 6.0 REMARK 210 IONIC STRENGTH : 50MM D11-TRIS-HCL, 2.2MM ZNCL2; REMARK 210 50MM D11-TRIS-HCL, 5.5MM ZNCL2 REMARK 210 PRESSURE : AMBIENT; AMBIENT REMARK 210 SAMPLE CONTENTS : 2MM ZFY-6T[Y10L]; 2MM ZFY REMARK 210 -6T[Y10L]; 5MM ZFY-6T[Y10L]; 5MM REMARK 210 ZFY-6T[Y10L] REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : 2D NOESY; DQF-COSY; 3D-TOCSY REMARK 210 -NOESY; 2D-ROESY REMARK 210 SPECTROMETER FIELD STRENGTH : 500 MHZ REMARK 210 SPECTROMETER MODEL : VXRS; UNITYPLUS; INOVA REMARK 210 SPECTROMETER MANUFACTURER : VARIAN REMARK 210 REMARK 210 STRUCTURE DETERMINATION. REMARK 210 SOFTWARE USED : VNMR 4.3, 5.3, NHFIT, DGII REMARK 210 STANDALONE REMARK 210 METHOD USED : DISTANCE GEOMETRY/SIMULATED REMARK 210 ANNEALING, FOLLOWED BY REMARK 210 RESTRAINED MOLECULAR DYNAMICS. REMARK 210 THE STEREOSPECIFIC ASSIGNMENTS REMARK 210 OF THE L10 METHYL GROUPS WERE REMARK 210 DETERMINED BY RELAXATION-MATRIX REMARK 210 NOE BACKCALCULATION. REMARK 210 REMARK 210 CONFORMERS, NUMBER CALCULATED : 50 REMARK 210 CONFORMERS, NUMBER SUBMITTED : 30 REMARK 210 CONFORMERS, SELECTION CRITERIA : STRUCTURES WITH THE LEAST REMARK 210 RESTRAINT VIOLATIONS REMARK 210 REMARK 210 BEST REPRESENTATIVE CONFORMER IN THIS ENSEMBLE : 6 REMARK 210 REMARK 210 REMARK: REMARK 210 THIS STRUCTURE WAS DETERMINED USING 2D AND 3D HOMONUCLEAR REMARK 210 TECHNIQUES.STEREOSPECIFIC ASSIGNMENTS FOR THE L18 METHYL GROUPS REMARK 210 COULD NOT BE UNAMBIGUOUSLY DETERMINED. HOWEVER, THE RESONANCES REMARK 210 WERE CLEARLY REMARK 210 RESOLVED. AS A RESULT,THE STRUCTURES WERE CALCULATED AS REMARK 210 TWO FAMILIES, DEPENDING ON THE ASSIGNMENTS USED. STRUCTURES 1-15 REMARK 210 BELONG TO ONE REMARK 210 FAMILY, AND USE THE ASSIGNMENTS INDICATED IN THE REMARK 210 ACCOMPANYING RESTRAINT FILE. STRUCTURES 16-30 USE THE OPPOSITE REMARK 210 ASSIGNMENTS FOR THE L18 REMARK 210 METHYLS. REMARK 215 REMARK 215 NMR STUDY REMARK 215 THE COORDINATES IN THIS ENTRY WERE GENERATED FROM SOLUTION REMARK 215 NMR DATA. PROTEIN DATA BANK CONVENTIONS REQUIRE THAT REMARK 215 CRYST1 AND SCALE RECORDS BE INCLUDED, BUT THE VALUES ON REMARK 215 THESE RECORDS ARE MEANINGLESS. 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 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CLOSE CONTACTS 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 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 1 CYS A 8 -116.47 -112.78 REMARK 500 1 GLU A 9 42.76 -164.08 REMARK 500 1 SER A 12 -83.84 -129.15 REMARK 500 1 ALA A 13 -66.99 -164.88 REMARK 500 1 SER A 16 -50.51 -15.39 REMARK 500 1 SER A 27 75.29 40.25 REMARK 500 1 LYS A 28 -87.34 8.12 REMARK 500 2 TYR A 7 -55.12 -132.62 REMARK 500 2 CYS A 8 -113.72 -111.72 REMARK 500 2 GLU A 9 43.64 -156.72 REMARK 500 3 THR A 2 -166.04 -117.38 REMARK 500 3 TYR A 7 -50.36 -121.38 REMARK 500 3 GLU A 9 66.80 118.68 REMARK 500 3 ASP A 14 -153.61 -137.24 REMARK 500 3 SER A 15 -55.92 -26.02 REMARK 500 3 SER A 16 -38.81 -33.37 REMARK 500 3 LYS A 25 -35.38 -142.21 REMARK 500 3 SER A 27 -59.33 78.47 REMARK 500 3 LYS A 28 -62.58 -130.79 REMARK 500 3 GLU A 29 69.69 28.32 REMARK 500 4 THR A 2 -163.65 -112.58 REMARK 500 4 TYR A 7 -50.45 -137.50 REMARK 500 4 CYS A 8 -124.35 -118.88 REMARK 500 4 GLU A 9 48.95 -157.06 REMARK 500 4 ASP A 14 -97.32 -122.42 REMARK 500 4 SER A 16 -155.31 50.21 REMARK 500 4 ASN A 17 -30.15 -25.43 REMARK 500 4 SER A 27 54.81 -109.24 REMARK 500 4 LYS A 28 74.74 7.00 REMARK 500 4 GLU A 29 60.38 10.31 REMARK 500 5 TYR A 7 -42.56 -131.66 REMARK 500 5 GLU A 9 -40.50 144.39 REMARK 500 5 LEU A 10 143.94 -24.90 REMARK 500 5 LEU A 18 -61.65 -109.21 REMARK 500 5 HIS A 21 -70.09 -43.77 REMARK 500 5 SER A 27 45.96 -89.58 REMARK 500 6 TYR A 7 -49.62 -139.57 REMARK 500 6 CYS A 8 -64.36 -107.18 REMARK 500 6 GLU A 9 52.39 143.72 REMARK 500 6 SER A 16 56.79 -96.82 REMARK 500 6 LYS A 28 -57.13 -141.12 REMARK 500 7 GLU A 9 -39.47 147.82 REMARK 500 7 LEU A 10 153.43 -29.92 REMARK 500 7 SER A 12 -162.87 -124.05 REMARK 500 7 ALA A 13 -63.71 -108.24 REMARK 500 7 LYS A 25 -36.62 -144.81 REMARK 500 7 HIS A 26 -61.17 -127.75 REMARK 500 7 SER A 27 -35.14 119.93 REMARK 500 7 LYS A 28 63.21 104.99 REMARK 500 7 GLU A 29 56.35 28.08 REMARK 500 REMARK 500 THIS ENTRY HAS 204 RAMACHANDRAN OUTLIERS. REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: PLANAR GROUPS REMARK 500 REMARK 500 PLANAR GROUPS IN THE FOLLOWING RESIDUES HAVE A TOTAL REMARK 500 RMS DISTANCE OF ALL ATOMS FROM THE BEST-FIT PLANE REMARK 500 BY MORE THAN AN EXPECTED VALUE OF 6*RMSD, WITH AN REMARK 500 RMSD 0.02 ANGSTROMS, OR AT LEAST ONE ATOM HAS REMARK 500 AN RMSD GREATER THAN THIS VALUE REMARK 500 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 500 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 M RES CSSEQI RMS TYPE REMARK 500 1 ARG A 11 0.32 SIDE CHAIN REMARK 500 3 ARG A 11 0.31 SIDE CHAIN REMARK 500 4 ARG A 11 0.31 SIDE CHAIN REMARK 500 5 ARG A 11 0.22 SIDE CHAIN REMARK 500 6 ARG A 11 0.08 SIDE CHAIN REMARK 500 7 ARG A 11 0.31 SIDE CHAIN REMARK 500 8 ARG A 11 0.28 SIDE CHAIN REMARK 500 9 ARG A 11 0.28 SIDE CHAIN REMARK 500 10 ARG A 11 0.18 SIDE CHAIN REMARK 500 11 ARG A 11 0.32 SIDE CHAIN REMARK 500 12 ARG A 11 0.28 SIDE CHAIN REMARK 500 13 ARG A 11 0.14 SIDE CHAIN REMARK 500 14 ARG A 11 0.23 SIDE CHAIN REMARK 500 15 ARG A 11 0.31 SIDE CHAIN REMARK 500 16 ARG A 11 0.24 SIDE CHAIN REMARK 500 17 ARG A 11 0.31 SIDE CHAIN REMARK 500 18 ARG A 11 0.31 SIDE CHAIN REMARK 500 19 ARG A 11 0.20 SIDE CHAIN REMARK 500 20 ARG A 11 0.28 SIDE CHAIN REMARK 500 21 ARG A 11 0.32 SIDE CHAIN REMARK 500 22 ARG A 11 0.28 SIDE CHAIN REMARK 500 23 ARG A 11 0.31 SIDE CHAIN REMARK 500 24 ARG A 11 0.23 SIDE CHAIN REMARK 500 25 ARG A 11 0.20 SIDE CHAIN REMARK 500 26 ARG A 11 0.17 SIDE CHAIN REMARK 500 27 ARG A 11 0.18 SIDE CHAIN REMARK 500 28 ARG A 11 0.13 SIDE CHAIN REMARK 500 29 ARG A 11 0.25 SIDE CHAIN REMARK 500 30 ARG A 11 0.32 SIDE CHAIN 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 31 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS A 5 SG REMARK 620 2 CYS A 8 SG 110.2 REMARK 620 3 HIS A 21 NE2 110.3 112.3 REMARK 620 4 HIS A 26 NE2 105.1 112.2 106.4 REMARK 620 N 1 2 3 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 31 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 5ZNF RELATED DB: PDB REMARK 900 5ZNF CONTAINS THE WILD-TYPE ZFY-6T ZINC FINGER REMARK 900 RELATED ID: 1KLR RELATED DB: PDB REMARK 900 1KLR CONTAINS THE Y10F MUTANT REMARK 999 REMARK 999 SEQUENCE REMARK 999 THE MUTATION Y10L WAS CREATED FOR STRUCTURAL REMARK 999 STUDIES. IN ADDITION, THE P2T MUTATION AND REMARK 999 C-TERMINAL K, ORIGINALLY INTRODUCED IN ZFY-6T REMARK 999 (PDB ENTRY 5ZNF) IMPROVE SAMPLE BEHAVIOR REMARK 999 WITHOUT AFFECTING STRUCTURE. DBREF 1KLS A 1 29 UNP P08048 ZFY_HUMAN 570 598 SEQADV 1KLS THR A 2 UNP P08048 PRO 571 ENGINEERED MUTATION SEQADV 1KLS LEU A 10 UNP P08048 TYR 579 ENGINEERED MUTATION SEQADV 1KLS LYS A 30 UNP P08048 SEE REMARK 999 SEQRES 1 A 30 LYS THR TYR GLN CYS GLN TYR CYS GLU LEU ARG SER ALA SEQRES 2 A 30 ASP SER SER ASN LEU LYS THR HIS ILE LYS THR LYS HIS SEQRES 3 A 30 SER LYS GLU LYS HET ZN A 31 1 HETNAM ZN ZINC ION FORMUL 2 ZN ZN 2+ HELIX 1 1 ASP A 14 HIS A 26 1 13 LINK SG CYS A 5 ZN ZN A 31 1555 1555 2.30 LINK SG CYS A 8 ZN ZN A 31 1555 1555 2.30 LINK NE2 HIS A 21 ZN ZN A 31 1555 1555 2.00 LINK NE2 HIS A 26 ZN ZN A 31 1555 1555 1.99 CISPEP 1 ALA A 13 ASP A 14 3 0.44 CISPEP 2 ALA A 13 ASP A 14 4 0.32 CISPEP 3 SER A 15 SER A 16 4 0.06 CISPEP 4 SER A 15 SER A 16 6 0.26 CISPEP 5 HIS A 26 SER A 27 13 0.40 CISPEP 6 LYS A 1 THR A 2 22 0.15 CISPEP 7 SER A 16 ASN A 17 23 0.49 CISPEP 8 LYS A 1 THR A 2 24 -0.06 CISPEP 9 SER A 15 SER A 16 25 0.02 CISPEP 10 GLU A 29 LYS A 30 25 -0.12 CISPEP 11 LYS A 19 THR A 20 26 0.68 CISPEP 12 GLU A 29 LYS A 30 30 -0.14 SITE 1 AC1 4 CYS A 5 CYS A 8 HIS A 21 HIS A 26 CRYST1 1.000 1.000 1.000 90.00 90.00 90.00 P 1 1 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 1.000000 0.000000 0.000000 0.00000 SCALE2 0.000000 1.000000 0.000000 0.00000 SCALE3 0.000000 0.000000 1.000000 0.00000 MODEL 1 MODEL 2 MODEL 3 MODEL 4 MODEL 5 MODEL 6 MODEL 7 MODEL 8 MODEL 9 MODEL 10 MODEL 11 MODEL 12 MODEL 13 MODEL 14 MODEL 15 MODEL 16 MODEL 17 MODEL 18 MODEL 19 MODEL 20 MODEL 21 MODEL 22 MODEL 23 MODEL 24 MODEL 25 MODEL 26 MODEL 27 MODEL 28 MODEL 29 MODEL 30