HEADER TRANSCRIPTION 12-DEC-01 1KLR TITLE NMR STRUCTURE OF THE ZFY-6T[Y10F] 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 25 AUTHOR M.J.LACHENMANN,J.E.LADBURY,N.B.PHILLIPS,N.NARAYANA,X.QIAN,M.A.WEISS REVDAT 3 27-OCT-21 1KLR 1 REMARK SEQADV LINK REVDAT 2 24-FEB-09 1KLR 1 VERSN REVDAT 1 13-MAR-02 1KLR 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 1 REMARK 1 REFERENCE 1 REMARK 1 AUTH X.QIAN,M.A.WEISS REMARK 1 TITL TWO-DIMENSIONAL NMR STUDIES OF THE ZINC FINGER MOTIF: REMARK 1 TITL 2 SOLUTION STRUCTURES AND DYNAMICS OF MUTANT ZFY DOMAINS REMARK 1 TITL 3 CONTAINING AROMATIC SUBSTITUTIONS IN THE HYDROPHOBIC CORE REMARK 1 REF BIOCHEMISTRY V. 31 7463 1992 REMARK 1 REFN ISSN 0006-2960 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: REMARK 3 STRUCTURES ARE BASED ON 229 INTERRESIDUE REMARK 3 NOE-DERIVED DISTANCE CONSTRAINTS, 24 DIHEDRAL REMARK 3 ANGLE RESTRAINTS, AND 10 HYDROGEN BOND RESTRAINTS. REMARK 4 REMARK 4 1KLR COMPLIES WITH FORMAT V. 3.15, 01-DEC-08 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 13-DEC-01. REMARK 100 THE DEPOSITION ID IS D_1000015086. 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[Y10F]; 2MM ZFY REMARK 210 -6T[Y10F]; 5MM ZFY-6T[Y10F]; 5MM REMARK 210 ZFY-6T[Y10F] 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 : NHFIT, DGII STANDALONE, VNMR 4.3 REMARK 210 -5.3 REMARK 210 METHOD USED : DISTANCE GEOMETRY/SIMULATED REMARK 210 ANNEALING, FOLLOWED BY REMARK 210 RESTRAINED MOLECULAR DYNAMICS. REMARK 210 REMARK 210 CONFORMERS, NUMBER CALCULATED : 52 REMARK 210 CONFORMERS, NUMBER SUBMITTED : 25 REMARK 210 CONFORMERS, SELECTION CRITERIA : STRUCTURES WITH THE LEAST REMARK 210 RESTRAINT VIOLATIONS REMARK 210 REMARK 210 BEST REPRESENTATIVE CONFORMER IN THIS ENSEMBLE : 14 REMARK 210 REMARK 210 REMARK: THIS STRUCTURE WAS DETERMINED USING REMARK 210 2D AND 3D HOMONUCLEAR TECHNIQUES. REMARK 210 THIS STRUCTURE REPRESENTS A REFINEMENT OF REMARK 210 THE STRUCTURE ORIGINALLY PUBLISHED IN REMARK 210 SECONDARY CITATION #1 (QIAN, X. AND WEISS, REMARK 210 M.A.). ADDITIONAL CONSTRAINTS WERE DETERMINED REMARK 210 USING HIGHER-CONCENTRATION SAMPLES AND BY REMARK 210 HOMONUCLEAR 3D-NMR METHODS. 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: 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 12 SER A 16 N - CA - C ANGL. DEV. = -17.5 DEGREES REMARK 500 13 SER A 16 N - CA - C ANGL. DEV. = 19.0 DEGREES REMARK 500 14 ARG A 11 NE - CZ - NH2 ANGL. DEV. = -3.5 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 1 TYR A 7 -56.38 -137.71 REMARK 500 1 CYS A 8 -160.43 -125.09 REMARK 500 1 GLU A 9 57.06 -103.55 REMARK 500 1 LYS A 28 -103.18 -98.97 REMARK 500 2 TYR A 7 -53.61 -131.83 REMARK 500 2 CYS A 8 -158.03 -124.04 REMARK 500 2 GLU A 9 55.65 -105.35 REMARK 500 2 SER A 15 -54.82 111.13 REMARK 500 2 LYS A 28 -58.66 109.19 REMARK 500 2 GLU A 29 66.82 12.59 REMARK 500 3 GLN A 6 43.62 -95.95 REMARK 500 3 TYR A 7 -54.68 -129.02 REMARK 500 3 CYS A 8 -164.24 -126.24 REMARK 500 3 GLU A 9 61.71 -107.25 REMARK 500 3 SER A 12 -24.14 -140.11 REMARK 500 3 ALA A 13 45.82 33.46 REMARK 500 3 ASP A 14 -61.07 -126.18 REMARK 500 3 SER A 15 -65.15 111.97 REMARK 500 3 LYS A 28 72.66 8.88 REMARK 500 4 GLN A 6 -35.44 116.67 REMARK 500 4 CYS A 8 -165.83 -113.25 REMARK 500 4 GLU A 9 50.93 -100.02 REMARK 500 4 ASP A 14 -69.63 -122.41 REMARK 500 4 SER A 15 -58.61 115.20 REMARK 500 4 LYS A 28 70.39 8.60 REMARK 500 5 TYR A 7 -50.76 -129.20 REMARK 500 5 CYS A 8 -164.96 -119.80 REMARK 500 5 GLU A 9 57.73 -108.68 REMARK 500 5 SER A 12 -65.13 -143.07 REMARK 500 5 ALA A 13 26.73 118.73 REMARK 500 5 SER A 27 -57.05 -137.52 REMARK 500 5 GLU A 29 -65.62 -7.97 REMARK 500 6 TYR A 7 -57.55 -140.96 REMARK 500 6 CYS A 8 -137.08 -116.76 REMARK 500 6 PHE A 10 118.27 -13.69 REMARK 500 6 HIS A 26 -73.55 -121.58 REMARK 500 7 TYR A 7 -58.71 -131.06 REMARK 500 7 CYS A 8 -154.94 -118.29 REMARK 500 7 GLU A 9 54.11 -109.45 REMARK 500 7 SER A 16 117.30 131.73 REMARK 500 7 ASN A 17 48.58 -88.16 REMARK 500 7 HIS A 26 -52.00 -123.12 REMARK 500 7 SER A 27 -146.71 -115.60 REMARK 500 7 LYS A 28 64.70 6.70 REMARK 500 7 GLU A 29 115.51 104.62 REMARK 500 8 TYR A 7 -58.48 -136.75 REMARK 500 8 CYS A 8 -161.60 -115.59 REMARK 500 8 GLU A 9 57.52 -109.86 REMARK 500 8 SER A 15 -61.60 117.98 REMARK 500 9 TYR A 7 -54.51 -136.82 REMARK 500 REMARK 500 THIS ENTRY HAS 152 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 0.31 SIDE CHAIN REMARK 500 2 ARG A 11 0.23 SIDE CHAIN REMARK 500 3 ARG A 11 0.29 SIDE CHAIN REMARK 500 4 ARG A 11 0.25 SIDE CHAIN REMARK 500 5 ARG A 11 0.30 SIDE CHAIN REMARK 500 6 ARG A 11 0.28 SIDE CHAIN REMARK 500 7 ARG A 11 0.20 SIDE CHAIN REMARK 500 8 ARG A 11 0.28 SIDE CHAIN REMARK 500 9 ARG A 11 0.26 SIDE CHAIN REMARK 500 10 ARG A 11 0.14 SIDE CHAIN REMARK 500 11 ARG A 11 0.25 SIDE CHAIN REMARK 500 12 ARG A 11 0.31 SIDE CHAIN REMARK 500 13 ARG A 11 0.31 SIDE CHAIN REMARK 500 14 ARG A 11 0.31 SIDE CHAIN REMARK 500 15 ARG A 11 0.31 SIDE CHAIN REMARK 500 16 ARG A 11 0.29 SIDE CHAIN REMARK 500 17 ARG A 11 0.26 SIDE CHAIN REMARK 500 18 ARG A 11 0.28 SIDE CHAIN REMARK 500 19 ARG A 11 0.31 SIDE CHAIN REMARK 500 20 ARG A 11 0.17 SIDE CHAIN REMARK 500 21 ARG A 11 0.08 SIDE CHAIN REMARK 500 22 ARG A 11 0.30 SIDE CHAIN REMARK 500 23 ARG A 11 0.25 SIDE CHAIN REMARK 500 24 ARG A 11 0.31 SIDE CHAIN REMARK 500 25 ARG A 11 0.31 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 111.4 REMARK 620 3 HIS A 21 NE2 109.6 111.5 REMARK 620 4 HIS A 26 NE2 106.1 111.2 106.8 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: 1KLS RELATED DB: PDB REMARK 900 1KLS CONTAINS THE Y10L MUTANT REMARK 999 REMARK 999 SEQUENCE REMARK 999 THE MUTATION Y10F 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 1KLR A 1 29 UNP P08048 ZFY_HUMAN 570 598 SEQADV 1KLR THR A 2 UNP P08048 PRO 571 ENGINEERED MUTATION SEQADV 1KLR PHE A 10 UNP P08048 TYR 579 ENGINEERED MUTATION SEQADV 1KLR LYS A 30 UNP P08048 SEE REMARK 999 SEQRES 1 A 30 LYS THR TYR GLN CYS GLN TYR CYS GLU PHE 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 SER A 15 HIS A 26 1 12 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 2.00 CISPEP 1 SER A 16 ASN A 17 7 0.76 CISPEP 2 SER A 15 SER A 16 10 -0.09 CISPEP 3 SER A 16 ASN A 17 10 0.81 CISPEP 4 LYS A 23 THR A 24 10 0.55 CISPEP 5 SER A 27 LYS A 28 10 0.48 CISPEP 6 SER A 16 ASN A 17 12 1.25 CISPEP 7 SER A 15 SER A 16 13 0.39 CISPEP 8 LYS A 1 THR A 2 20 0.09 CISPEP 9 SER A 27 LYS A 28 20 -0.23 CISPEP 10 LYS A 1 THR A 2 21 -0.02 CISPEP 11 LYS A 23 THR A 24 22 0.42 CISPEP 12 LYS A 1 THR A 2 24 0.01 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