HEADER HYDROLASE/STRUCTURAL PROTEIN 17-AUG-14 4W5A TITLE COMPLEX STRUCTURE OF ATRX ADD BOUND TO H3K9ME3S10PH PEPTIDE COMPND MOL_ID: 1; COMPND 2 MOLECULE: TRANSCRIPTIONAL REGULATOR ATRX; COMPND 3 CHAIN: A, B, E; COMPND 4 FRAGMENT: UNP RESIDUES 167-289; COMPND 5 SYNONYM: ATP-DEPENDENT HELICASE ATRX,X-LINKED HELICASE II,X-LINKED COMPND 6 NUCLEAR PROTEIN,XNP,ZNF-HX; COMPND 7 EC: 3.6.4.12; COMPND 8 ENGINEERED: YES; COMPND 9 MUTATION: YES; COMPND 10 MOL_ID: 2; COMPND 11 MOLECULE: PEPTIDE FROM HISTONE H3.3; COMPND 12 CHAIN: C, D, F; COMPND 13 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 3 ORGANISM_COMMON: HUMAN; SOURCE 4 ORGANISM_TAXID: 9606; SOURCE 5 GENE: ATRX, RAD54L, XH2; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 8 EXPRESSION_SYSTEM_STRAIN: BL21(DE3); SOURCE 9 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 10 EXPRESSION_SYSTEM_PLASMID: PGOOD6P; SOURCE 11 MOL_ID: 2; SOURCE 12 SYNTHETIC: YES; SOURCE 13 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 14 ORGANISM_COMMON: HUMAN; SOURCE 15 ORGANISM_TAXID: 9606 KEYWDS EPIGENETIC REGULATION, COMPLEX, TRANSCRIPTION, MITOSIS, HYDROLASE- KEYWDS 2 STRUCTURAL PROTEIN COMPLEX EXPDTA X-RAY DIFFRACTION AUTHOR D.ZHAO,B.XIANG,H.LI REVDAT 3 08-NOV-23 4W5A 1 SOURCE KEYWDS JRNL REMARK REVDAT 2 17-JUN-15 4W5A 1 JRNL REVDAT 1 21-JAN-15 4W5A 0 JRNL AUTH K.M.NOH,I.MAZE,D.ZHAO,B.XIANG,W.WENDERSKI,P.W.LEWIS,L.SHEN, JRNL AUTH 2 H.LI,C.D.ALLIS JRNL TITL ATRX TOLERATES ACTIVITY-DEPENDENT HISTONE H3 METHYL/PHOS JRNL TITL 2 SWITCHING TO MAINTAIN REPETITIVE ELEMENT SILENCING IN JRNL TITL 3 NEURONS JRNL REF PROC.NATL.ACAD.SCI.USA V. 112 6820 2015 JRNL REFN ESSN 1091-6490 JRNL PMID 25538301 JRNL DOI 10.1073/PNAS.1411258112 REMARK 2 REMARK 2 RESOLUTION. 2.60 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX (PHENIX.REFINE: 1.9_1692) REMARK 3 AUTHORS : PAUL ADAMS,PAVEL AFONINE,VINCENT CHEN,IAN REMARK 3 : DAVIS,KRESHNA GOPAL,RALF GROSSE-KUNSTLEVE, REMARK 3 : LI-WEI HUNG,ROBERT IMMORMINO,TOM IOERGER, REMARK 3 : AIRLIE MCCOY,ERIK MCKEE,NIGEL MORIARTY, REMARK 3 : REETAL PAI,RANDY READ,JANE RICHARDSON, REMARK 3 : DAVID RICHARDSON,TOD ROMO,JIM SACCHETTINI, REMARK 3 : NICHOLAS SAUTER,JACOB SMITH,LAURENT REMARK 3 : STORONI,TOM TERWILLIGER,PETER ZWART REMARK 3 REMARK 3 REFINEMENT TARGET : ML REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.60 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 37.50 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.4 REMARK 3 NUMBER OF REFLECTIONS : 14463 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.224 REMARK 3 R VALUE (WORKING SET) : 0.221 REMARK 3 FREE R VALUE : 0.260 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 7.680 REMARK 3 FREE R VALUE TEST SET COUNT : 1111 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT (IN BINS). REMARK 3 BIN RESOLUTION RANGE COMPL. NWORK NFREE RWORK RFREE REMARK 3 1 37.6000 - 5.1900 0.99 1786 139 0.2158 0.2400 REMARK 3 2 5.1932 - 4.1237 0.99 1681 130 0.1917 0.2209 REMARK 3 3 4.1237 - 3.6029 1.00 1685 135 0.1971 0.2347 REMARK 3 4 3.6029 - 3.2737 1.00 1618 149 0.2289 0.2633 REMARK 3 5 3.2737 - 3.0392 1.00 1712 118 0.2598 0.3247 REMARK 3 6 3.0392 - 2.8601 1.00 1658 133 0.2766 0.3333 REMARK 3 7 2.8601 - 2.7169 1.00 1613 150 0.2692 0.3631 REMARK 3 8 2.7169 - 2.5986 0.98 1599 157 0.2906 0.3528 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : FLAT BULK SOLVENT MODEL REMARK 3 SOLVENT RADIUS : 1.11 REMARK 3 SHRINKAGE RADIUS : 0.90 REMARK 3 K_SOL : NULL REMARK 3 B_SOL : NULL REMARK 3 REMARK 3 ERROR ESTIMATES. REMARK 3 COORDINATE ERROR (MAXIMUM-LIKELIHOOD BASED) : 0.390 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 29.710 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 62.80 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 69.40 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 TWINNING INFORMATION. REMARK 3 FRACTION: NULL REMARK 3 OPERATOR: NULL REMARK 3 REMARK 3 DEVIATIONS FROM IDEAL VALUES. REMARK 3 RMSD COUNT REMARK 3 BOND : 0.003 3257 REMARK 3 ANGLE : 0.800 4396 REMARK 3 CHIRALITY : 0.029 468 REMARK 3 PLANARITY : 0.003 567 REMARK 3 DIHEDRAL : 15.450 1210 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : NULL REMARK 3 REMARK 3 NCS DETAILS REMARK 3 NUMBER OF NCS GROUPS : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 4W5A COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 10-SEP-14. REMARK 100 THE DEPOSITION ID IS D_1000203218. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 14-APR-12 REMARK 200 TEMPERATURE (KELVIN) : 110 REMARK 200 PH : 6.0 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : SSRF REMARK 200 BEAMLINE : BL17U REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.97892 REMARK 200 MONOCHROMATOR : SI(111) DOUBLE CRYSTAL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 315R REMARK 200 INTENSITY-INTEGRATION SOFTWARE : NULL REMARK 200 DATA SCALING SOFTWARE : NULL REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 14504 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.600 REMARK 200 RESOLUTION RANGE LOW (A) : 50.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : -3.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.6 REMARK 200 DATA REDUNDANCY : 8.300 REMARK 200 R MERGE (I) : 0.09600 REMARK 200 R SYM (I) : 0.09600 REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 26.1000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.60 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.64 REMARK 200 COMPLETENESS FOR SHELL (%) : 100.0 REMARK 200 DATA REDUNDANCY IN SHELL : 8.50 REMARK 200 R MERGE FOR SHELL (I) : 0.75600 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 <I/SIGMA(I)> FOR SHELL : 3.500 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: MOLREP REMARK 200 STARTING MODEL: 3QL9 REMARK 200 REMARK 200 REMARK: HEXAGONAL ROD-LIKE REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 46.31 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.29 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 13-20% PEG 4000, 0.1 M MES, 3 MM REMARK 280 MGCL2, VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 277K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 32 2 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -Y,X-Y,Z+2/3 REMARK 290 3555 -X+Y,-X,Z+1/3 REMARK 290 4555 Y,X,-Z REMARK 290 5555 X-Y,-Y,-Z+1/3 REMARK 290 6555 -X,-X+Y,-Z+2/3 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 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 2 0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 91.73267 REMARK 290 SMTRY1 3 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 3 -0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 45.86633 REMARK 290 SMTRY1 4 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 4 0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 4 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 5 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 5 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 5 0.000000 0.000000 -1.000000 45.86633 REMARK 290 SMTRY1 6 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 6 -0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 6 0.000000 0.000000 -1.000000 91.73267 REMARK 290 REMARK 290 REMARK: NULL REMARK 300 REMARK 300 BIOMOLECULE: 1, 2, 3 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: DIMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 1390 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 8310 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -5.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, C 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 350 REMARK 350 BIOMOLECULE: 2 REMARK 350 AUTHOR DETERMINED BIOLOGICAL UNIT: DIMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 1350 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 8310 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -5.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: B, D 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 350 REMARK 350 BIOMOLECULE: 3 REMARK 350 AUTHOR DETERMINED BIOLOGICAL UNIT: DIMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 1410 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 7480 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -3.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: E, F 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 465 REMARK 465 MISSING RESIDUES REMARK 465 THE FOLLOWING RESIDUES WERE NOT LOCATED IN THE REMARK 465 EXPERIMENT. (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 465 IDENTIFIER; SSSEQ=SEQUENCE NUMBER; I=INSERTION CODE.) REMARK 465 REMARK 465 M RES C SSSEQI REMARK 465 GLN A 129 REMARK 465 GLY C 12 REMARK 465 GLY C 13 REMARK 465 LYS C 14 REMARK 465 ALA C 15 REMARK 465 LEU B 127 REMARK 465 GLU B 128 REMARK 465 GLN B 129 REMARK 465 GLY D 13 REMARK 465 LYS D 14 REMARK 465 ALA D 15 REMARK 465 GLY E 1 REMARK 465 PRO E 2 REMARK 465 LEU E 3 REMARK 465 GLY E 4 REMARK 465 SER E 5 REMARK 465 MET E 6 REMARK 465 GLY E 7 REMARK 465 HIS E 20 REMARK 465 PHE E 21 REMARK 465 GLN E 22 REMARK 465 LYS E 23 REMARK 465 ASP E 24 REMARK 465 SER E 25 REMARK 465 GLU E 128 REMARK 465 GLN E 129 REMARK 465 GLY F 12 REMARK 465 GLY F 13 REMARK 465 LYS F 14 REMARK 465 ALA F 15 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 GLN B 22 CG CD OE1 NE2 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 ASP A 52 -164.55 -100.75 REMARK 500 MET A 97 36.74 -81.08 REMARK 500 LEU A 127 21.32 -77.14 REMARK 500 LYS B 23 -159.25 -85.27 REMARK 500 GLN B 33 15.87 59.60 REMARK 500 ASN B 100 56.17 -107.03 REMARK 500 SEP D 10 12.15 -68.41 REMARK 500 CYS E 75 -160.93 -111.82 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 501 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS A 11 SG REMARK 620 2 CYS A 14 SG 110.4 REMARK 620 3 CYS A 37 SG 111.1 119.0 REMARK 620 4 CYS A 40 SG 108.9 103.1 103.4 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 ZN A 502 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS A 60 SG REMARK 620 2 CYS A 63 SG 108.2 REMARK 620 3 CYS A 80 SG 112.7 114.3 REMARK 620 4 CYS A 83 SG 111.1 107.4 103.0 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 ZN A 503 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS A 72 SG REMARK 620 2 CYS A 75 SG 109.5 REMARK 620 3 CYS A 105 SG 102.1 98.3 REMARK 620 4 CYS A 108 SG 117.4 117.7 108.9 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 ZN B 501 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS B 11 SG REMARK 620 2 CYS B 14 SG 111.2 REMARK 620 3 CYS B 37 SG 107.0 121.0 REMARK 620 4 CYS B 40 SG 113.5 103.7 100.0 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 ZN B 502 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS B 60 SG REMARK 620 2 CYS B 63 SG 111.4 REMARK 620 3 CYS B 80 SG 105.3 113.3 REMARK 620 4 CYS B 83 SG 115.4 107.1 104.2 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 ZN B 503 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS B 72 SG REMARK 620 2 CYS B 75 SG 109.6 REMARK 620 3 CYS B 105 SG 105.8 98.5 REMARK 620 4 CYS B 108 SG 118.5 112.8 109.6 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 ZN E 501 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS E 11 SG REMARK 620 2 CYS E 14 SG 103.9 REMARK 620 3 CYS E 37 SG 104.7 115.6 REMARK 620 4 CYS E 40 SG 107.3 108.1 116.2 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 ZN E 502 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS E 60 SG REMARK 620 2 CYS E 63 SG 112.0 REMARK 620 3 CYS E 80 SG 101.1 120.7 REMARK 620 4 CYS E 83 SG 116.5 106.8 99.6 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 ZN E 503 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS E 72 SG REMARK 620 2 CYS E 75 SG 109.8 REMARK 620 3 CYS E 105 SG 109.1 103.8 REMARK 620 4 CYS E 108 SG 120.2 100.9 111.5 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 501 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue ZN A 502 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue ZN A 503 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue ZN B 501 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue ZN B 502 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue ZN B 503 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC7 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue ZN E 501 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC8 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue ZN E 502 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC9 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue ZN E 503 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 3QL9 RELATED DB: PDB REMARK 900 STRUCTURE OF HUMAN ATRX ADD IN COMPLEX WITH H3K9(1-15)ME3 PEPTIDE REMARK 900 IN MONOCLINIC CRYSTAL FORM. REMARK 900 RELATED ID: 3QLA RELATED DB: PDB REMARK 900 STRUCTURE OF HUMAN ATRX ADD DOMAIN IN COMPLEX WITH H3K9(1-15)ME3 REMARK 900 PEPTIDE IN HEXAGONAL CRYSTAL FORM. REMARK 900 RELATED ID: 3QLN RELATED DB: PDB REMARK 900 STRUCTURE OF HUMAN ATRX ADD IN ITS FREE STATE. REMARK 900 RELATED ID: 3QLC RELATED DB: PDB REMARK 900 STRUCTURE OF HUMAN ATRX ADD IN COMPLEX WITH UNMODIFIED H3(1-15) REMARK 900 PEPTIDE. DBREF 4W5A A 7 129 UNP P46100 ATRX_HUMAN 167 289 DBREF 4W5A C 1 15 UNP P84243 H33_HUMAN 2 16 DBREF 4W5A B 7 129 UNP P46100 ATRX_HUMAN 167 289 DBREF 4W5A D 1 15 UNP P84243 H33_HUMAN 2 16 DBREF 4W5A E 7 129 UNP P46100 ATRX_HUMAN 167 289 DBREF 4W5A F 1 15 UNP P84243 H33_HUMAN 2 16 SEQADV 4W5A GLY A 1 UNP P46100 EXPRESSION TAG SEQADV 4W5A PRO A 2 UNP P46100 EXPRESSION TAG SEQADV 4W5A LEU A 3 UNP P46100 EXPRESSION TAG SEQADV 4W5A GLY A 4 UNP P46100 EXPRESSION TAG SEQADV 4W5A SER A 5 UNP P46100 EXPRESSION TAG SEQADV 4W5A MET A 6 UNP P46100 EXPRESSION TAG SEQADV 4W5A ARG A 91 UNP P46100 LYS 251 ENGINEERED MUTATION SEQADV 4W5A TYR A 124 UNP P46100 PHE 284 ENGINEERED MUTATION SEQADV 4W5A GLY B 1 UNP P46100 EXPRESSION TAG SEQADV 4W5A PRO B 2 UNP P46100 EXPRESSION TAG SEQADV 4W5A LEU B 3 UNP P46100 EXPRESSION TAG SEQADV 4W5A GLY B 4 UNP P46100 EXPRESSION TAG SEQADV 4W5A SER B 5 UNP P46100 EXPRESSION TAG SEQADV 4W5A MET B 6 UNP P46100 EXPRESSION TAG SEQADV 4W5A ARG B 91 UNP P46100 LYS 251 ENGINEERED MUTATION SEQADV 4W5A TYR B 124 UNP P46100 PHE 284 ENGINEERED MUTATION SEQADV 4W5A GLY E 1 UNP P46100 EXPRESSION TAG SEQADV 4W5A PRO E 2 UNP P46100 EXPRESSION TAG SEQADV 4W5A LEU E 3 UNP P46100 EXPRESSION TAG SEQADV 4W5A GLY E 4 UNP P46100 EXPRESSION TAG SEQADV 4W5A SER E 5 UNP P46100 EXPRESSION TAG SEQADV 4W5A MET E 6 UNP P46100 EXPRESSION TAG SEQADV 4W5A ARG E 91 UNP P46100 LYS 251 ENGINEERED MUTATION SEQADV 4W5A TYR E 124 UNP P46100 PHE 284 ENGINEERED MUTATION SEQRES 1 A 129 GLY PRO LEU GLY SER MET GLY ILE VAL SER CYS THR ALA SEQRES 2 A 129 CYS GLY GLN GLN VAL ASN HIS PHE GLN LYS ASP SER ILE SEQRES 3 A 129 TYR ARG HIS PRO SER LEU GLN VAL LEU ILE CYS LYS ASN SEQRES 4 A 129 CYS PHE LYS TYR TYR MET SER ASP ASP ILE SER ARG ASP SEQRES 5 A 129 SER ASP GLY MET ASP GLU GLN CYS ARG TRP CYS ALA GLU SEQRES 6 A 129 GLY GLY ASN LEU ILE CYS CYS ASP PHE CYS HIS ASN ALA SEQRES 7 A 129 PHE CYS LYS LYS CYS ILE LEU ARG ASN LEU GLY ARG ARG SEQRES 8 A 129 GLU LEU SER THR ILE MET ASP GLU ASN ASN GLN TRP TYR SEQRES 9 A 129 CYS TYR ILE CYS HIS PRO GLU PRO LEU LEU ASP LEU VAL SEQRES 10 A 129 THR ALA CYS ASN SER VAL TYR GLU ASN LEU GLU GLN SEQRES 1 C 15 ALA ARG THR LYS GLN THR ALA ARG M3L SEP THR GLY GLY SEQRES 2 C 15 LYS ALA SEQRES 1 B 129 GLY PRO LEU GLY SER MET GLY ILE VAL SER CYS THR ALA SEQRES 2 B 129 CYS GLY GLN GLN VAL ASN HIS PHE GLN LYS ASP SER ILE SEQRES 3 B 129 TYR ARG HIS PRO SER LEU GLN VAL LEU ILE CYS LYS ASN SEQRES 4 B 129 CYS PHE LYS TYR TYR MET SER ASP ASP ILE SER ARG ASP SEQRES 5 B 129 SER ASP GLY MET ASP GLU GLN CYS ARG TRP CYS ALA GLU SEQRES 6 B 129 GLY GLY ASN LEU ILE CYS CYS ASP PHE CYS HIS ASN ALA SEQRES 7 B 129 PHE CYS LYS LYS CYS ILE LEU ARG ASN LEU GLY ARG ARG SEQRES 8 B 129 GLU LEU SER THR ILE MET ASP GLU ASN ASN GLN TRP TYR SEQRES 9 B 129 CYS TYR ILE CYS HIS PRO GLU PRO LEU LEU ASP LEU VAL SEQRES 10 B 129 THR ALA CYS ASN SER VAL TYR GLU ASN LEU GLU GLN SEQRES 1 D 15 ALA ARG THR LYS GLN THR ALA ARG M3L SEP THR GLY GLY SEQRES 2 D 15 LYS ALA SEQRES 1 E 129 GLY PRO LEU GLY SER MET GLY ILE VAL SER CYS THR ALA SEQRES 2 E 129 CYS GLY GLN GLN VAL ASN HIS PHE GLN LYS ASP SER ILE SEQRES 3 E 129 TYR ARG HIS PRO SER LEU GLN VAL LEU ILE CYS LYS ASN SEQRES 4 E 129 CYS PHE LYS TYR TYR MET SER ASP ASP ILE SER ARG ASP SEQRES 5 E 129 SER ASP GLY MET ASP GLU GLN CYS ARG TRP CYS ALA GLU SEQRES 6 E 129 GLY GLY ASN LEU ILE CYS CYS ASP PHE CYS HIS ASN ALA SEQRES 7 E 129 PHE CYS LYS LYS CYS ILE LEU ARG ASN LEU GLY ARG ARG SEQRES 8 E 129 GLU LEU SER THR ILE MET ASP GLU ASN ASN GLN TRP TYR SEQRES 9 E 129 CYS TYR ILE CYS HIS PRO GLU PRO LEU LEU ASP LEU VAL SEQRES 10 E 129 THR ALA CYS ASN SER VAL TYR GLU ASN LEU GLU GLN SEQRES 1 F 15 ALA ARG THR LYS GLN THR ALA ARG M3L SEP THR GLY GLY SEQRES 2 F 15 LYS ALA MODRES 4W5A M3L C 9 LYS MODIFIED RESIDUE MODRES 4W5A SEP C 10 SER MODIFIED RESIDUE MODRES 4W5A M3L D 9 LYS MODIFIED RESIDUE MODRES 4W5A SEP D 10 SER MODIFIED RESIDUE MODRES 4W5A M3L F 9 LYS MODIFIED RESIDUE MODRES 4W5A SEP F 10 SER MODIFIED RESIDUE HET M3L C 9 12 HET SEP C 10 10 HET M3L D 9 12 HET SEP D 10 10 HET M3L F 9 12 HET SEP F 10 10 HET ZN A 501 1 HET ZN A 502 1 HET ZN A 503 1 HET ZN B 501 1 HET ZN B 502 1 HET ZN B 503 1 HET ZN E 501 1 HET ZN E 502 1 HET ZN E 503 1 HETNAM M3L N-TRIMETHYLLYSINE HETNAM SEP PHOSPHOSERINE HETNAM ZN ZINC ION HETSYN SEP PHOSPHONOSERINE FORMUL 2 M3L 3(C9 H21 N2 O2 1+) FORMUL 2 SEP 3(C3 H8 N O6 P) FORMUL 7 ZN 9(ZN 2+) FORMUL 16 HOH *19(H2 O) HELIX 1 AA1 CYS A 37 ASP A 47 1 11 HELIX 2 AA2 LYS A 81 GLY A 89 1 9 HELIX 3 AA3 GLY A 89 MET A 97 1 9 HELIX 4 AA4 PRO A 110 PRO A 112 5 3 HELIX 5 AA5 LEU A 113 LEU A 127 1 15 HELIX 6 AA6 LYS B 38 MET B 45 1 8 HELIX 7 AA7 LYS B 81 LEU B 88 1 8 HELIX 8 AA8 GLY B 89 MET B 97 1 9 HELIX 9 AA9 PRO B 110 PRO B 112 5 3 HELIX 10 AB1 LEU B 113 ASN B 126 1 14 HELIX 11 AB2 CYS E 37 MET E 45 1 9 HELIX 12 AB3 LYS E 81 ASP E 98 1 18 HELIX 13 AB4 PRO E 110 PRO E 112 5 3 HELIX 14 AB5 LEU E 113 LEU E 127 1 15 SHEET 1 AA1 2 VAL A 9 SER A 10 0 SHEET 2 AA1 2 GLN A 17 VAL A 18 -1 O VAL A 18 N VAL A 9 SHEET 1 AA2 2 TYR A 27 ARG A 28 0 SHEET 2 AA2 2 LEU A 35 ILE A 36 -1 O ILE A 36 N TYR A 27 SHEET 1 AA3 3 ALA A 78 CYS A 80 0 SHEET 2 AA3 3 ASN A 68 CYS A 71 -1 N ILE A 70 O PHE A 79 SHEET 3 AA3 3 ARG C 2 GLN C 5 -1 O LYS C 4 N LEU A 69 SHEET 1 AA4 2 ILE B 26 ARG B 28 0 SHEET 2 AA4 2 LEU B 35 CYS B 37 -1 O ILE B 36 N TYR B 27 SHEET 1 AA5 3 ALA B 78 CYS B 80 0 SHEET 2 AA5 3 ASN B 68 CYS B 71 -1 N ILE B 70 O PHE B 79 SHEET 3 AA5 3 ARG D 2 GLN D 5 -1 O ARG D 2 N CYS B 71 SHEET 1 AA6 2 VAL E 9 SER E 10 0 SHEET 2 AA6 2 GLN E 17 VAL E 18 -1 O VAL E 18 N VAL E 9 SHEET 1 AA7 2 TYR E 27 ARG E 28 0 SHEET 2 AA7 2 LEU E 35 ILE E 36 -1 O ILE E 36 N TYR E 27 SHEET 1 AA8 3 ALA E 78 CYS E 80 0 SHEET 2 AA8 3 ASN E 68 CYS E 71 -1 N ILE E 70 O PHE E 79 SHEET 3 AA8 3 ARG F 2 GLN F 5 -1 O LYS F 4 N LEU E 69 LINK C ARG C 8 N M3L C 9 1555 1555 1.33 LINK C M3L C 9 N SEP C 10 1555 1555 1.33 LINK C SEP C 10 N THR C 11 1555 1555 1.33 LINK C ARG D 8 N M3L D 9 1555 1555 1.33 LINK C M3L D 9 N SEP D 10 1555 1555 1.33 LINK C SEP D 10 N THR D 11 1555 1555 1.33 LINK C ARG F 8 N M3L F 9 1555 1555 1.33 LINK C M3L F 9 N SEP F 10 1555 1555 1.33 LINK C SEP F 10 N THR F 11 1555 1555 1.33 LINK SG CYS A 11 ZN ZN A 501 1555 1555 2.24 LINK SG CYS A 14 ZN ZN A 501 1555 1555 2.30 LINK SG CYS A 37 ZN ZN A 501 1555 1555 2.42 LINK SG CYS A 40 ZN ZN A 501 1555 1555 2.35 LINK SG CYS A 60 ZN ZN A 502 1555 1555 2.45 LINK SG CYS A 63 ZN ZN A 502 1555 1555 2.45 LINK SG CYS A 72 ZN ZN A 503 1555 1555 2.33 LINK SG CYS A 75 ZN ZN A 503 1555 1555 2.26 LINK SG CYS A 80 ZN ZN A 502 1555 1555 2.31 LINK SG CYS A 83 ZN ZN A 502 1555 1555 2.31 LINK SG CYS A 105 ZN ZN A 503 1555 1555 2.37 LINK SG CYS A 108 ZN ZN A 503 1555 1555 2.28 LINK SG CYS B 11 ZN ZN B 501 1555 1555 2.35 LINK SG CYS B 14 ZN ZN B 501 1555 1555 2.29 LINK SG CYS B 37 ZN ZN B 501 1555 1555 2.35 LINK SG CYS B 40 ZN ZN B 501 1555 1555 2.37 LINK SG CYS B 60 ZN ZN B 502 1555 1555 2.45 LINK SG CYS B 63 ZN ZN B 502 1555 1555 2.34 LINK SG CYS B 72 ZN ZN B 503 1555 1555 2.26 LINK SG CYS B 75 ZN ZN B 503 1555 1555 2.30 LINK SG CYS B 80 ZN ZN B 502 1555 1555 2.27 LINK SG CYS B 83 ZN ZN B 502 1555 1555 2.27 LINK SG CYS B 105 ZN ZN B 503 1555 1555 2.43 LINK SG CYS B 108 ZN ZN B 503 1555 1555 2.28 LINK SG CYS E 11 ZN ZN E 501 1555 1555 2.52 LINK SG CYS E 14 ZN ZN E 501 1555 1555 2.53 LINK SG CYS E 37 ZN ZN E 501 1555 1555 2.37 LINK SG CYS E 40 ZN ZN E 501 1555 1555 2.52 LINK SG CYS E 60 ZN ZN E 502 1555 1555 2.69 LINK SG CYS E 63 ZN ZN E 502 1555 1555 2.40 LINK SG CYS E 72 ZN ZN E 503 1555 1555 2.66 LINK SG CYS E 75 ZN ZN E 503 1555 1555 2.41 LINK SG CYS E 80 ZN ZN E 502 1555 1555 2.61 LINK SG CYS E 83 ZN ZN E 502 1555 1555 2.51 LINK SG CYS E 105 ZN ZN E 503 1555 1555 2.43 LINK SG CYS E 108 ZN ZN E 503 1555 1555 2.53 CISPEP 1 PHE B 21 GLN B 22 0 -3.32 SITE 1 AC1 4 CYS A 11 CYS A 14 CYS A 37 CYS A 40 SITE 1 AC2 4 CYS A 60 CYS A 63 CYS A 80 CYS A 83 SITE 1 AC3 4 CYS A 72 CYS A 75 CYS A 105 CYS A 108 SITE 1 AC4 4 CYS B 11 CYS B 14 CYS B 37 CYS B 40 SITE 1 AC5 4 CYS B 60 CYS B 63 CYS B 80 CYS B 83 SITE 1 AC6 4 CYS B 72 CYS B 75 CYS B 105 CYS B 108 SITE 1 AC7 4 CYS E 11 CYS E 14 CYS E 37 CYS E 40 SITE 1 AC8 4 CYS E 60 CYS E 63 CYS E 80 CYS E 83 SITE 1 AC9 4 CYS E 72 CYS E 75 CYS E 105 CYS E 108 CRYST1 75.522 75.522 137.599 90.00 90.00 120.00 P 32 2 1 18 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 0.013241 0.007645 0.000000 0.00000 SCALE2 0.000000 0.015290 0.000000 0.00000 SCALE3 0.000000 0.000000 0.007267 0.00000