HEADER TRANSCRIPTION 17-OCT-04 1XRZ TITLE NMR STRUCTURE OF A ZINC FINGER WITH CYCLOHEXANYLALANINE SUBSTITUTED TITLE 2 FOR THE CENTRAL AROMATIC RESIDUE COMPND MOL_ID: 1; COMPND 2 MOLECULE: ZINC FINGER Y-CHROMOSOMAL PROTEIN; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: SEQUENCE DATABASE RESIDUES 570-598: CONTAINS C2H2-TYPE 6 COMPND 5 ZINC FINGER (RESIDUES 572-595); COMPND 6 SYNONYM: ZINC FINGER 6; COMPND 7 ENGINEERED: YES; COMPND 8 MUTATION: YES SOURCE MOL_ID: 1; SOURCE 2 SYNTHETIC: YES; SOURCE 3 OTHER_DETAILS: THE PROTEIN WAS CHEMICALLY SYNTHESIZED USING SOLID- SOURCE 4 PHASE PEPTIDE SYNTHESIS. THE ZFY PROTEIN IS NATURALLY FOUND IN HOMO SOURCE 5 SAPIENS (HUMAN). KEYWDS CYCLOHEXANYLALANINE, ZINC FINGER, TRANSCRIPTION EXPDTA SOLUTION NMR NUMMDL 34 AUTHOR M.J.LACHENMANN,J.E.LADBURY,X.QIAN,K.HUANG,R.SINGH,M.A.WEISS REVDAT 3 20-OCT-21 1XRZ 1 REMARK SEQADV LINK REVDAT 2 24-FEB-09 1XRZ 1 VERSN REVDAT 1 30-NOV-04 1XRZ 0 JRNL AUTH M.J.LACHENMANN,J.E.LADBURY,X.QIAN,K.HUANG,R.SINGH,M.A.WEISS JRNL TITL SOLVATION AND THE HIDDEN THERMODYNAMICS OF A ZINC FINGER JRNL TITL 2 PROBED BY NONSTANDARD REPAIR OF A PROTEIN CREVICE JRNL REF PROTEIN SCI. V. 13 3115 2004 JRNL REFN ISSN 0961-8368 JRNL PMID 15557258 JRNL DOI 10.1110/PS.04866404 REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : VNMR 4.3, X-PLOR 3.1 REMARK 3 AUTHORS : VARIAN, INC. (VNMR), BRUNGER (X-PLOR) REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 1XRZ COMPLIES WITH FORMAT V. 3.15, 01-DEC-08 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 12-NOV-04. REMARK 100 THE DEPOSITION ID IS D_1000030698. REMARK 210 REMARK 210 EXPERIMENTAL DETAILS REMARK 210 EXPERIMENT TYPE : NMR REMARK 210 TEMPERATURE (KELVIN) : 298 REMARK 210 PH : 6.0 REMARK 210 IONIC STRENGTH : 50MM D11-TRIS-HCL, 2.2MM ZNCL2 REMARK 210 PRESSURE : AMBIENT REMARK 210 SAMPLE CONTENTS : 2MM ZFY-6T[Y10(CHA)], 90% H2O, REMARK 210 10% D2O; 2MM ZFY-6T[Y10(CHA)], REMARK 210 100% D2O REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : DQF-COSY; 2D TOCSY; 2D NOESY REMARK 210 SPECTROMETER FIELD STRENGTH : 500 MHZ REMARK 210 SPECTROMETER MODEL : VXRS; UNITYPLUS REMARK 210 SPECTROMETER MANUFACTURER : VARIAN REMARK 210 REMARK 210 STRUCTURE DETERMINATION. REMARK 210 SOFTWARE USED : VNMR 5.3, DGII STANDALONE, NHFIT REMARK 210 STANDALONE REMARK 210 METHOD USED : DISTANCE GEOMETRY/SIMULATED REMARK 210 ANNEALING FOLLOWED BY RESTRAINED REMARK 210 MOLECULAR DYNAMICS REMARK 210 REMARK 210 CONFORMERS, NUMBER CALCULATED : 50 REMARK 210 CONFORMERS, NUMBER SUBMITTED : 34 REMARK 210 CONFORMERS, SELECTION CRITERIA : STRUCTURES WITH THE LEAST REMARK 210 RESTRAINT VIOLATIONS REMARK 210 REMARK 210 BEST REPRESENTATIVE CONFORMER IN THIS ENSEMBLE : 1 REMARK 210 REMARK 210 REMARK: THIS STRUCTURE WAS DETERMINED USING STANDARD 2D REMARK 210 HOMONUCLEAR TECHNIQUES. HYDROGEN ASSIGNMENTS FOR THE REMARK 210 CYCLOHEXANYL RING WERE MADE BY EXTENSION FROM THE NORMAL 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: 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 5 144.84 -35.20 REMARK 500 1 GLN A 6 30.45 -99.56 REMARK 500 1 TYR A 7 -50.36 -140.50 REMARK 500 1 CYS A 8 -159.98 -117.53 REMARK 500 1 GLU A 9 57.30 -116.64 REMARK 500 1 SER A 15 -60.38 -95.88 REMARK 500 2 CYS A 8 -163.74 -122.74 REMARK 500 2 GLU A 9 60.22 -116.57 REMARK 500 2 LYS A 28 -59.29 -121.76 REMARK 500 3 CYS A 5 171.66 -57.59 REMARK 500 3 CYS A 8 -161.08 -117.11 REMARK 500 3 GLU A 9 57.12 -116.82 REMARK 500 3 SER A 27 -113.58 3.46 REMARK 500 3 GLU A 29 -58.03 -15.55 REMARK 500 4 CYS A 5 162.00 -44.00 REMARK 500 4 TYR A 7 -53.79 -136.58 REMARK 500 4 CYS A 8 -158.48 -113.10 REMARK 500 4 GLU A 9 57.74 -114.92 REMARK 500 4 SER A 15 -60.21 -93.19 REMARK 500 4 SER A 27 86.54 -12.11 REMARK 500 4 LYS A 28 -178.02 58.65 REMARK 500 5 TYR A 7 -50.19 -133.28 REMARK 500 5 CYS A 8 -161.78 -121.49 REMARK 500 5 GLU A 9 57.53 -115.77 REMARK 500 5 ALA A 13 -31.57 94.79 REMARK 500 5 LYS A 23 -30.59 -39.69 REMARK 500 5 SER A 27 -74.67 33.11 REMARK 500 6 CYS A 8 -164.20 -112.93 REMARK 500 6 GLU A 9 58.18 -109.69 REMARK 500 6 ASP A 14 -69.81 -141.00 REMARK 500 6 SER A 15 -63.27 137.91 REMARK 500 6 LYS A 23 -7.91 -58.54 REMARK 500 7 TYR A 7 -46.80 -133.79 REMARK 500 7 CYS A 8 -159.51 -118.90 REMARK 500 7 GLU A 9 55.69 -112.77 REMARK 500 7 SER A 27 97.19 22.80 REMARK 500 7 GLU A 29 -60.65 -132.14 REMARK 500 8 CYS A 5 -179.19 -62.94 REMARK 500 8 CYS A 8 -164.32 -112.70 REMARK 500 8 GLU A 9 59.05 -114.93 REMARK 500 8 HIS A 26 -57.27 -123.27 REMARK 500 9 THR A 2 168.10 104.17 REMARK 500 9 TYR A 7 -50.28 -138.35 REMARK 500 9 CYS A 8 -158.08 -123.78 REMARK 500 9 GLU A 9 55.32 -115.92 REMARK 500 9 SER A 16 -52.85 -129.85 REMARK 500 9 SER A 27 -71.02 -17.26 REMARK 500 9 LYS A 28 -65.24 -124.59 REMARK 500 9 GLU A 29 91.53 21.67 REMARK 500 10 TYR A 7 -42.58 -133.45 REMARK 500 REMARK 500 THIS ENTRY HAS 188 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 0.23 SIDE CHAIN REMARK 500 2 ARG A 11 0.26 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 0.30 SIDE CHAIN REMARK 500 6 ARG A 11 0.31 SIDE CHAIN REMARK 500 7 ARG A 11 0.30 SIDE CHAIN REMARK 500 8 ARG A 11 0.27 SIDE CHAIN REMARK 500 9 ARG A 11 0.23 SIDE CHAIN REMARK 500 10 ARG A 11 0.29 SIDE CHAIN REMARK 500 11 ARG A 11 0.28 SIDE CHAIN REMARK 500 12 ARG A 11 0.21 SIDE CHAIN REMARK 500 13 ARG A 11 0.29 SIDE CHAIN REMARK 500 14 ARG A 11 0.30 SIDE CHAIN REMARK 500 15 ARG A 11 0.29 SIDE CHAIN REMARK 500 16 ARG A 11 0.31 SIDE CHAIN REMARK 500 17 ARG A 11 0.29 SIDE CHAIN REMARK 500 18 ARG A 11 0.32 SIDE CHAIN REMARK 500 19 ARG A 11 0.29 SIDE CHAIN REMARK 500 20 ARG A 11 0.25 SIDE CHAIN REMARK 500 21 ARG A 11 0.32 SIDE CHAIN REMARK 500 22 ARG A 11 0.15 SIDE CHAIN REMARK 500 23 ARG A 11 0.32 SIDE CHAIN REMARK 500 24 ARG A 11 0.23 SIDE CHAIN REMARK 500 25 ARG A 11 0.28 SIDE CHAIN REMARK 500 26 ARG A 11 0.20 SIDE CHAIN REMARK 500 27 ARG A 11 0.21 SIDE CHAIN REMARK 500 28 ARG A 11 0.26 SIDE CHAIN REMARK 500 29 ARG A 11 0.30 SIDE CHAIN REMARK 500 30 ARG A 11 0.27 SIDE CHAIN REMARK 500 31 ARG A 11 0.31 SIDE CHAIN REMARK 500 32 ARG A 11 0.32 SIDE CHAIN REMARK 500 33 ARG A 11 0.20 SIDE CHAIN REMARK 500 34 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 108.5 REMARK 620 3 HIS A 21 NE2 111.1 111.3 REMARK 620 4 HIS A 26 NE2 107.9 112.3 105.6 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 CONTAINS THE WILD-TYPE ZFY-6T FINGER REMARK 900 RELATED ID: 1KLS RELATED DB: PDB REMARK 900 CONTAINS THE ZFY-6T[Y10L] MUTANT REMARK 900 RELATED ID: 1KLR RELATED DB: PDB REMARK 900 CONTAINS THE ZFY-6T[Y10F] MUTANT REMARK 999 REMARK 999 SEQUENCE REMARK 999 LYS A 30 WAS ENGINEERED TO IMPROVE SAMPLE SOLUBILITY REMARK 999 WHILE NOT AFFECTING THE STRUCTURE DBREF 1XRZ A 1 29 UNP P08048 ZFY_HUMAN 570 598 SEQADV 1XRZ THR A 2 UNP P08048 PRO 571 ENGINEERED MUTATION SEQADV 1XRZ ALC A 10 UNP P08048 TYR 579 ENGINEERED MUTATION SEQADV 1XRZ LYS A 30 UNP P08048 SEE REMARK 999 SEQRES 1 A 30 LYS THR TYR GLN CYS GLN TYR CYS GLU ALC 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 MODRES 1XRZ ALC A 10 ALA 2-AMINO-3-CYCLOHEXYL-PROPIONIC ACID HET ALC A 10 26 HET ZN A 31 1 HETNAM ALC 2-AMINO-3-CYCLOHEXYL-PROPIONIC ACID HETNAM ZN ZINC ION FORMUL 1 ALC C9 H17 N O2 FORMUL 2 ZN ZN 2+ HELIX 1 1 ASP A 14 HIS A 26 1 13 SHEET 1 A 2 TYR A 3 GLN A 4 0 SHEET 2 A 2 ARG A 11 SER A 12 -1 O SER A 12 N TYR A 3 LINK C GLU A 9 N ALC A 10 1555 1555 1.31 LINK C ALC A 10 N ARG A 11 1555 1555 1.31 LINK SG CYS A 5 ZN ZN A 31 1555 1555 2.30 LINK SG CYS A 8 ZN ZN A 31 1555 1555 2.29 LINK NE2 HIS A 21 ZN ZN A 31 1555 1555 1.99 LINK NE2 HIS A 26 ZN ZN A 31 1555 1555 1.99 CISPEP 1 GLU A 29 LYS A 30 1 -0.03 CISPEP 2 GLU A 29 LYS A 30 5 0.19 CISPEP 3 SER A 27 LYS A 28 17 -0.17 CISPEP 4 LYS A 28 GLU A 29 18 -0.06 CISPEP 5 GLU A 29 LYS A 30 20 0.07 CISPEP 6 SER A 15 SER A 16 21 0.20 CISPEP 7 LYS A 28 GLU A 29 22 -0.04 CISPEP 8 SER A 27 LYS A 28 26 -0.15 CISPEP 9 GLU A 29 LYS A 30 28 0.18 CISPEP 10 GLU A 29 LYS A 30 31 -0.19 CISPEP 11 LYS A 1 THR A 2 32 0.04 CISPEP 12 LYS A 1 THR A 2 33 -0.06 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 MODEL 31 MODEL 32 MODEL 33 MODEL 34