10 20 30 40 50 60 70 80 1XRZ - Header ----|----|----|----|----|----|----|----|----|----|----|----|----|----|----|----| Asymmetric UnitHEADER TRANSCRIPTION 17-OCT-04 1XRZ
TITLE NMR STRUCTURE OF A ZINC FINGER WITH CYCLOHEXANYLALANINE TITLE 2 SUBSTITUTED 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 COMPND 5 C2H2-TYPE 6 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 SOURCE 4 USING SOLID-PHASE PEPTIDE SYNTHESIS. THE ZFY PROTEIN IS SOURCE 5 NATURALLY FOUND IN HOMO 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 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, JRNL AUTH 2 M.A.WEISS JRNL TITL SOLVATION AND THE HIDDEN THERMODYNAMICS OF A ZINC JRNL TITL 2 FINGER PROBED BY NONSTANDARD REPAIR OF A PROTEIN JRNL TITL 3 CREVICE JRNL REF PROTEIN SCI. V. 13 3115 2004 JRNL REFN ISSN 0961-8368 JRNL PMID 15557258 JRNL DOI 10.1110/PS.04866404
REMARK 1
REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE.
REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : X-PLOR 3.1 REMARK 3 AUTHORS : BRUNGER 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 RCSB ID CODE IS RCSB030698.
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% REMARK 210 H2O, 10% D2O; 2MM ZFY- REMARK 210 6T[Y10(CHA)], 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 4.3, VNMR 5.3, DGII REMARK 210 STANDALONE, NHFIT STANDALONE REMARK 210 METHOD USED : DISTANCE GEOMETRY/SIMULATED REMARK 210 ANNEALING FOLLOWED BY REMARK 210 RESTRAINED 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 REMARK 210 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 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 SER A 15 -60.38 -95.88 REMARK 500 2 CYS A 8 -163.74 -122.74 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 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 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 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 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 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 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 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 10 CYS A 8 -160.81 -117.76 REMARK 500 10 SER A 16 -50.39 -131.91 REMARK 500 10 SER A 27 90.88 -4.18 REMARK 500 11 CYS A 5 159.07 -48.49 REMARK 500 11 TYR A 7 -55.28 -144.58 REMARK 500 11 CYS A 8 -158.03 -117.86 REMARK 500 11 LYS A 23 -37.27 -35.89 REMARK 500 11 SER A 27 -168.33 -106.14 REMARK 500 12 TYR A 7 -49.58 -140.28 REMARK 500 12 CYS A 8 -162.49 -117.84 REMARK 500 12 ASP A 14 -59.67 -125.86 REMARK 500 12 SER A 15 -36.31 123.77 REMARK 500 12 LYS A 23 -35.57 -36.98 REMARK 500 12 SER A 27 59.54 17.40 REMARK 500 13 TYR A 7 -52.47 -122.81 REMARK 500 13 CYS A 8 -158.23 -115.52 REMARK 500 13 SER A 27 -72.43 64.40 REMARK 500 14 CYS A 8 -163.43 -116.73 REMARK 500 14 GLU A 29 53.09 -109.66 REMARK 500 15 CYS A 8 -162.88 -114.31 REMARK 500 15 SER A 15 -63.10 -104.62 REMARK 500 15 LYS A 23 -38.67 -39.75 REMARK 500 15 SER A 27 169.41 112.28 REMARK 500 15 LYS A 28 -58.02 -122.13 REMARK 500 15 GLU A 29 -51.78 -126.36 REMARK 500 16 TYR A 7 -52.05 -137.04 REMARK 500 16 CYS A 8 -161.45 -115.34 REMARK 500 16 SER A 27 -168.74 -106.43 REMARK 500 16 GLU A 29 152.92 -47.84 REMARK 500 17 TYR A 7 -48.70 -142.18 REMARK 500 17 CYS A 8 -159.92 -119.66 REMARK 500 17 ALA A 13 -45.20 120.72 REMARK 500 17 LYS A 28 -71.33 -121.68 REMARK 500 17 GLU A 29 -50.99 -129.85 REMARK 500 18 TYR A 7 -48.20 -130.36 REMARK 500 18 CYS A 8 -160.21 -119.65 REMARK 500 18 LYS A 28 108.33 -19.97 REMARK 500 19 CYS A 8 -160.91 -115.22 REMARK 500 19 ASP A 14 -55.40 -138.92 REMARK 500 19 SER A 15 170.88 123.24 REMARK 500 19 SER A 16 -51.19 103.25 REMARK 500 19 GLU A 29 -141.89 -113.41 REMARK 500 20 TYR A 7 -51.20 -130.75 REMARK 500 20 CYS A 8 -160.07 -118.87 REMARK 500 20 SER A 12 -64.85 -131.67 REMARK 500 20 ALA A 13 -48.92 128.30 REMARK 500 20 SER A 15 51.48 -107.36 REMARK 500 20 SER A 16 -61.52 -127.09 REMARK 500 20 SER A 27 60.02 26.89 REMARK 500 21 CYS A 8 -163.84 -112.79 REMARK 500 21 SER A 16 46.57 -98.42 REMARK 500 21 SER A 27 40.01 33.96 REMARK 500 22 THR A 2 165.86 100.53 REMARK 500 22 CYS A 5 157.64 -36.92 REMARK 500 22 TYR A 7 -55.35 -146.44 REMARK 500 22 CYS A 8 -160.20 -111.57 REMARK 500 22 SER A 16 -16.05 -49.92 REMARK 500 22 SER A 27 -64.76 -97.33 REMARK 500 23 THR A 2 162.95 61.68 REMARK 500 23 CYS A 8 -158.52 -113.35 REMARK 500 23 SER A 16 -52.32 -131.16 REMARK 500 23 SER A 27 66.05 -110.83 REMARK 500 24 TYR A 7 -42.27 -139.55 REMARK 500 24 CYS A 8 -161.67 -121.63 REMARK 500 24 SER A 15 51.04 -114.68 REMARK 500 24 SER A 16 -46.37 -131.86 REMARK 500 24 LYS A 28 -164.48 -110.47 REMARK 500 25 TYR A 7 -48.08 -136.03 REMARK 500 25 CYS A 8 -163.43 -118.17 REMARK 500 25 ALA A 13 -36.14 120.29 REMARK 500 25 SER A 16 -61.22 -126.99 REMARK 500 25 SER A 27 24.75 45.91 REMARK 500 25 GLU A 29 -60.63 -10.13 REMARK 500 26 CYS A 8 -159.46 -117.76 REMARK 500 26 ALA A 13 28.39 -142.65 REMARK 500 26 ASP A 14 -62.42 -129.66 REMARK 500 26 SER A 15 -60.50 124.72 REMARK 500 27 TYR A 7 -49.39 -132.93 REMARK 500 27 CYS A 8 -160.05 -123.26 REMARK 500 27 ASP A 14 -63.90 -134.60 REMARK 500 27 SER A 15 -49.82 134.98 REMARK 500 27 LYS A 25 -32.01 -145.15 REMARK 500 27 SER A 27 56.04 -113.85 REMARK 500 27 LYS A 28 158.19 112.14 REMARK 500 27 GLU A 29 -66.17 -128.33 REMARK 500 28 TYR A 7 -49.52 -131.17 REMARK 500 28 CYS A 8 -160.76 -109.88 REMARK 500 28 LYS A 28 88.16 -28.36 REMARK 500 28 GLU A 29 146.50 5.35 REMARK 500 29 CYS A 8 -162.02 -118.21 REMARK 500 29 SER A 12 -60.74 -120.00 REMARK 500 29 ALA A 13 -14.59 107.86 REMARK 500 29 SER A 27 70.15 -14.50 REMARK 500 30 CYS A 5 164.15 -46.53 REMARK 500 30 TYR A 7 -54.73 -138.35 REMARK 500 30 CYS A 8 -128.98 -114.65 REMARK 500 30 ASP A 14 -66.09 -141.55 REMARK 500 30 SER A 15 -60.33 123.13 REMARK 500 30 HIS A 26 43.38 -100.16 REMARK 500 31 TYR A 7 -52.26 -138.57 REMARK 500 31 CYS A 8 -158.02 -115.87 REMARK 500 31 SER A 27 46.55 -108.74 REMARK 500 31 LYS A 28 124.04 -9.20 REMARK 500 32 CYS A 5 174.35 -52.01 REMARK 500 32 CYS A 8 -160.45 -112.52 REMARK 500 32 SER A 27 -177.26 119.13 REMARK 500 32 LYS A 28 161.07 95.07 REMARK 500 33 CYS A 8 -162.93 -116.22 REMARK 500 33 SER A 27 -76.46 5.50 REMARK 500 33 GLU A 29 71.64 6.71 REMARK 500 34 CYS A 5 154.05 -34.07 REMARK 500 34 TYR A 7 -53.21 -135.32 REMARK 500 34 CYS A 8 -159.84 -114.18 REMARK 500 34 ASP A 14 -66.85 -133.77 REMARK 500 34 SER A 15 -63.71 123.44 REMARK 500 34 SER A 27 76.61 24.31 REMARK 500 34 LYS A 28 -77.71 -7.20 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 1 ZN A 31 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HIS A 26 NE2 REMARK 620 2 HIS A 21 NE2 105.6 REMARK 620 3 CYS A 5 SG 107.9 111.1 REMARK 620 4 CYS A 8 SG 112.3 111.3 108.5 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 SEQADV 1XRZ ALC A 10 UNP P08048 TYR 579 ENGINEERED 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 NE2 HIS A 26 ZN ZN A 31 1555 1555 1.99 LINK NE2 HIS A 21 ZN ZN A 31 1555 1555 1.99 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 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
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