HEADER OXIDOREDUCTASE 30-NOV-17 6F4R TITLE HUMAN JMJD5 (N308C) IN COMPLEX WITH MN(II), NOG AND RCCD1 (139-143) TITLE 2 (COMPLEX-3) COMPND MOL_ID: 1; COMPND 2 MOLECULE: JMJC DOMAIN-CONTAINING PROTEIN 5; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: JUMONJI DOMAIN-CONTAINING PROTEIN 5,LYSINE-SPECIFIC COMPND 5 DEMETHYLASE 8; COMPND 6 EC: 1.14.11.47; COMPND 7 ENGINEERED: YES; COMPND 8 MUTATION: YES; COMPND 9 OTHER_DETAILS: CATALYTIC DOMAIN (RESIDUES 183-416); COMPND 10 MOL_ID: 2; COMPND 11 MOLECULE: RCC1 DOMAIN-CONTAINING PROTEIN 1; COMPND 12 CHAIN: B; COMPND 13 ENGINEERED: YES; COMPND 14 OTHER_DETAILS: FRAGMENT: 139-143 SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 3 ORGANISM_COMMON: HUMAN; SOURCE 4 ORGANISM_TAXID: 9606; SOURCE 5 GENE: KDM8, JMJD5; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21(DE3); SOURCE 7 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 8 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 9 EXPRESSION_SYSTEM_PLASMID: PNIC28 BSA4; SOURCE 10 MOL_ID: 2; SOURCE 11 SYNTHETIC: YES; SOURCE 12 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 13 ORGANISM_COMMON: HUMAN; SOURCE 14 ORGANISM_TAXID: 9606 KEYWDS OXIDOREDUCTASE, NON-HEME, IRON, 2-OXOGLUTARATE, DIOXYGENASE, JMJC, KEYWDS 2 JMJC DOMAIN, LYSINE-SPECIFIC DEMETHYLASE 8, JMJC DOMAIN-CONTAINING KEYWDS 3 PROTEIN 5, ARGINYL C-3 HYDROXYLASE, JMJD5, KDM8, OXYGENASE, HYPOXIA, KEYWDS 4 DNA-BINDING, METAL-BINDING, TRANSLATION, DSBH, FACIAL TRIAD, KEYWDS 5 CYTOPLASM, JMJC HYDROXYLASE, JMJC DEMETHYLASE, KDMS, POST- KEYWDS 6 TRANSLATIONAL MODIFICATIONS, PTM, BETA-HYDROXYLATION, HYDROXYLATION, KEYWDS 7 ARGININE HYDROXYLATION, RCC1 DOMAIN-CONTAINING PROTEIN 1, RCCD1, KEYWDS 8 REGULATOR OF CHROMOSOME CONDENSATION, 40S RIBOSOMAL PROTEIN S6, KEYWDS 9 RPS6, RIBOSOME BIOGENESIS, TRANSCRIPTION, EPIGENETIC REGULATION, KEYWDS 10 SIGNALING, DEVELOPMENT, CELL STRUCTURE, TRANSCRIPTION KEYWDS 11 ACTIVATOR/INHIBITOR, PHOSPHORYLATION, CANCER, POLYMORPHISM EXPDTA X-RAY DIFFRACTION AUTHOR R.CHOWDHURY,M.S.ISLAM,C.J.SCHOFIELD REVDAT 3 17-JAN-24 6F4R 1 LINK REVDAT 2 12-JUN-19 6F4R 1 AUTHOR REVDAT 1 04-APR-18 6F4R 0 JRNL AUTH S.E.WILKINS,S.ISLAM,J.M.GANNON,S.MARKOLOVIC,R.J.HOPKINSON, JRNL AUTH 2 W.GE,C.J.SCHOFIELD,R.CHOWDHURY JRNL TITL JMJD5 IS A HUMAN ARGINYL C-3 HYDROXYLASE. JRNL REF NAT COMMUN V. 9 1180 2018 JRNL REFN ESSN 2041-1723 JRNL PMID 29563586 JRNL DOI 10.1038/S41467-018-03410-W REMARK 2 REMARK 2 RESOLUTION. 1.30 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX (1.12_2829: ???) 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) : 1.30 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 49.84 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.340 REMARK 3 COMPLETENESS FOR RANGE (%) : 98.9 REMARK 3 NUMBER OF REFLECTIONS : 62039 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.144 REMARK 3 R VALUE (WORKING SET) : 0.143 REMARK 3 FREE R VALUE : 0.162 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.910 REMARK 3 FREE R VALUE TEST SET COUNT : 3045 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 49.8802 - 3.6333 1.00 2913 154 0.1539 0.1778 REMARK 3 2 3.6333 - 2.8840 1.00 2777 147 0.1289 0.1484 REMARK 3 3 2.8840 - 2.5194 1.00 2748 156 0.1322 0.1460 REMARK 3 4 2.5194 - 2.2891 1.00 2739 154 0.1257 0.1497 REMARK 3 5 2.2891 - 2.1250 1.00 2753 125 0.1238 0.1385 REMARK 3 6 2.1250 - 1.9997 1.00 2706 144 0.1174 0.1217 REMARK 3 7 1.9997 - 1.8996 1.00 2705 141 0.1175 0.1386 REMARK 3 8 1.8996 - 1.8169 1.00 2703 147 0.1291 0.1472 REMARK 3 9 1.8169 - 1.7469 1.00 2704 131 0.1336 0.1850 REMARK 3 10 1.7469 - 1.6866 1.00 2732 111 0.1326 0.1225 REMARK 3 11 1.6866 - 1.6339 1.00 2716 123 0.1336 0.1620 REMARK 3 12 1.6339 - 1.5872 1.00 2679 138 0.1398 0.1600 REMARK 3 13 1.5872 - 1.5454 1.00 2685 133 0.1482 0.1731 REMARK 3 14 1.5454 - 1.5077 1.00 2672 160 0.1520 0.1550 REMARK 3 15 1.5077 - 1.4734 1.00 2671 171 0.1688 0.2040 REMARK 3 16 1.4734 - 1.4421 1.00 2650 156 0.1847 0.1947 REMARK 3 17 1.4421 - 1.4132 1.00 2709 107 0.2069 0.2169 REMARK 3 18 1.4132 - 1.3865 1.00 2688 139 0.2132 0.2351 REMARK 3 19 1.3865 - 1.3618 1.00 2676 133 0.2307 0.2155 REMARK 3 20 1.3618 - 1.3387 1.00 2648 143 0.2407 0.2626 REMARK 3 21 1.3387 - 1.3171 1.00 2715 131 0.2493 0.3107 REMARK 3 22 1.3171 - 1.2968 0.76 2005 101 0.2715 0.2872 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : FLAT MODEL REMARK 3 SOLVENT RADIUS : 1.11 REMARK 3 SHRINKAGE RADIUS : 0.90 REMARK 3 K_SOL : 0.41 REMARK 3 B_SOL : 54.20 REMARK 3 REMARK 3 ERROR ESTIMATES. REMARK 3 COORDINATE ERROR (MAXIMUM-LIKELIHOOD BASED) : 0.120 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 15.500 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 15.50 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 24.00 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -1.91000 REMARK 3 B22 (A**2) : -0.52000 REMARK 3 B33 (A**2) : 2.43000 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : 0.00000 REMARK 3 B23 (A**2) : 0.00000 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 : 0.016 2345 REMARK 3 ANGLE : 1.401 3232 REMARK 3 CHIRALITY : 0.100 330 REMARK 3 PLANARITY : 0.011 438 REMARK 3 DIHEDRAL : 15.683 886 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : 1 REMARK 3 TLS GROUP : 1 REMARK 3 SELECTION: ALL REMARK 3 ORIGIN FOR THE GROUP (A): -39.9383 13.3208 98.6075 REMARK 3 T TENSOR REMARK 3 T11: 0.1089 T22: 0.1054 REMARK 3 T33: 0.1108 T12: 0.0024 REMARK 3 T13: 0.0037 T23: 0.0104 REMARK 3 L TENSOR REMARK 3 L11: 0.5733 L22: 0.8792 REMARK 3 L33: 0.9149 L12: 0.1841 REMARK 3 L13: -0.0143 L23: 0.4876 REMARK 3 S TENSOR REMARK 3 S11: -0.0124 S12: -0.0024 S13: -0.0411 REMARK 3 S21: -0.0111 S22: 0.0306 S23: -0.0232 REMARK 3 S31: -0.0019 S32: 0.0241 S33: 0.0011 REMARK 3 REMARK 3 NCS DETAILS REMARK 3 NUMBER OF NCS GROUPS : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: REFINEMENT TARGET : ML AND BULK SOLVENT REMARK 3 MODELLING METHOD USED: FLAT MODEL REMARK 4 REMARK 4 6F4R COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 30-NOV-17. REMARK 100 THE DEPOSITION ID IS D_1200007741. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 19-JAN-16 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 5.8 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : DIAMOND REMARK 200 BEAMLINE : I03 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.9795 REMARK 200 MONOCHROMATOR : SI 111 REMARK 200 OPTICS : MIRRORS REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS PILATUS3 6M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 706E REMARK 200 DATA SCALING SOFTWARE : HKL-2000 706E REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 62115 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.300 REMARK 200 RESOLUTION RANGE LOW (A) : 49.840 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 100.0 REMARK 200 DATA REDUNDANCY : 9.000 REMARK 200 R MERGE (I) : 0.07900 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 24.3000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.30 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.35 REMARK 200 COMPLETENESS FOR SHELL (%) : 100.0 REMARK 200 DATA REDUNDANCY IN SHELL : 8.80 REMARK 200 R MERGE FOR SHELL (I) : 1.20000 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 1.700 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: PHASER REMARK 200 STARTING MODEL: 6F4P REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 46.18 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.28 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.1M BIS-TRIS PH 5.8, 25 % PEG3350, REMARK 280 0.002 M MNCL2, 300 NL SITTING DROPS (SAMPLE:WELL, 1:1 RATIO), REMARK 280 VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 298K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 21 21 21 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X+1/2,-Y,Z+1/2 REMARK 290 3555 -X,Y+1/2,-Z+1/2 REMARK 290 4555 X+1/2,-Y+1/2,-Z 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 -1.000000 0.000000 0.000000 24.71450 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 38.99100 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 32.40500 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 38.99100 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 24.71450 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 32.40500 REMARK 290 SMTRY3 4 0.000000 0.000000 -1.000000 0.00000 REMARK 290 REMARK 290 REMARK: NULL REMARK 300 REMARK 300 BIOMOLECULE: 1, 2 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 350 REMARK 350 BIOMOLECULE: 2 REMARK 350 AUTHOR DETERMINED BIOLOGICAL UNIT: MONOMERIC REMARK 350 APPLY THE FOLLOWING TO CHAINS: B 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 HIS A 162 REMARK 465 HIS A 163 REMARK 465 HIS A 164 REMARK 465 HIS A 165 REMARK 465 HIS A 166 REMARK 465 HIS A 167 REMARK 465 SER A 168 REMARK 465 SER A 169 REMARK 465 GLY A 170 REMARK 465 VAL A 171 REMARK 465 ASP A 172 REMARK 465 LEU A 173 REMARK 465 GLY A 174 REMARK 465 THR A 175 REMARK 465 GLU A 176 REMARK 465 ASN A 177 REMARK 465 LEU A 178 REMARK 465 TYR A 179 REMARK 465 PHE A 180 REMARK 465 GLN A 181 REMARK 465 TYR B 143 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 A 219 CD OE1 NE2 REMARK 470 GLU A 247 CG CD OE1 OE2 REMARK 470 LYS A 378 CG CD CE NZ REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CLOSE CONTACTS IN SAME ASYMMETRIC UNIT 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 O VAL A 201 H32 TRS A 503 1.53 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: COVALENT BOND LENGTHS 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,2(A3,1X,A1,I4,A1,1X,A4,3X),1X,F6.3) 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 RES CSSEQI ATM2 DEVIATION REMARK 500 ASN A 359 CA ASN A 359 CB 0.168 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 ARG A 189 60.76 37.37 REMARK 500 PHE A 199 -55.00 -129.20 REMARK 500 PHE A 199 -55.00 -132.38 REMARK 500 ILE A 263 -62.35 -122.15 REMARK 500 ILE A 263 -66.57 -124.00 REMARK 500 GLU A 266 98.68 -47.59 REMARK 500 ASN A 367 65.29 -150.80 REMARK 500 REMARK 500 REMARK: NULL REMARK 525 REMARK 525 SOLVENT REMARK 525 REMARK 525 THE SOLVENT MOLECULES HAVE CHAIN IDENTIFIERS THAT REMARK 525 INDICATE THE POLYMER CHAIN WITH WHICH THEY ARE MOST REMARK 525 CLOSELY ASSOCIATED. THE REMARK LISTS ALL THE SOLVENT REMARK 525 MOLECULES WHICH ARE MORE THAN 5A AWAY FROM THE REMARK 525 NEAREST POLYMER CHAIN (M = MODEL NUMBER; REMARK 525 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE REMARK 525 NUMBER; I=INSERTION CODE): REMARK 525 REMARK 525 M RES CSSEQI REMARK 525 HOH A 953 DISTANCE = 5.93 ANGSTROMS REMARK 525 HOH A 954 DISTANCE = 6.04 ANGSTROMS REMARK 525 HOH A 955 DISTANCE = 6.80 ANGSTROMS REMARK 525 HOH A 956 DISTANCE = 6.81 ANGSTROMS REMARK 525 HOH A 957 DISTANCE = 6.90 ANGSTROMS 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 MN A 501 MN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HIS A 321 NE2 REMARK 620 2 ASP A 323 OD2 106.4 REMARK 620 3 HIS A 400 NE2 83.6 84.2 REMARK 620 4 OGA A 502 O2 161.7 91.7 100.6 REMARK 620 5 OGA A 502 O2' 87.3 165.2 92.2 74.8 REMARK 620 6 HOH A 749 O 86.1 87.5 164.4 92.9 99.0 REMARK 620 N 1 2 3 4 5 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue MN A 501 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue OGA A 502 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue TRS A 503 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 6F4M RELATED DB: PDB REMARK 900 RELATED ID: 6F4N RELATED DB: PDB REMARK 900 RELATED ID: 6F4O RELATED DB: PDB REMARK 900 RELATED ID: 6F4P RELATED DB: PDB REMARK 900 RELATED ID: 6F4Q RELATED DB: PDB REMARK 900 RELATED ID: 6F4S RELATED DB: PDB REMARK 900 RELATED ID: 6F4T RELATED DB: PDB DBREF 6F4R A 183 416 UNP Q8N371 KDM8_HUMAN 183 416 DBREF 6F4R B 139 143 UNP A6NED2 RCCD1_HUMAN 139 143 SEQADV 6F4R HIS A 162 UNP Q8N371 EXPRESSION TAG SEQADV 6F4R HIS A 163 UNP Q8N371 EXPRESSION TAG SEQADV 6F4R HIS A 164 UNP Q8N371 EXPRESSION TAG SEQADV 6F4R HIS A 165 UNP Q8N371 EXPRESSION TAG SEQADV 6F4R HIS A 166 UNP Q8N371 EXPRESSION TAG SEQADV 6F4R HIS A 167 UNP Q8N371 EXPRESSION TAG SEQADV 6F4R SER A 168 UNP Q8N371 EXPRESSION TAG SEQADV 6F4R SER A 169 UNP Q8N371 EXPRESSION TAG SEQADV 6F4R GLY A 170 UNP Q8N371 EXPRESSION TAG SEQADV 6F4R VAL A 171 UNP Q8N371 EXPRESSION TAG SEQADV 6F4R ASP A 172 UNP Q8N371 EXPRESSION TAG SEQADV 6F4R LEU A 173 UNP Q8N371 EXPRESSION TAG SEQADV 6F4R GLY A 174 UNP Q8N371 EXPRESSION TAG SEQADV 6F4R THR A 175 UNP Q8N371 EXPRESSION TAG SEQADV 6F4R GLU A 176 UNP Q8N371 EXPRESSION TAG SEQADV 6F4R ASN A 177 UNP Q8N371 EXPRESSION TAG SEQADV 6F4R LEU A 178 UNP Q8N371 EXPRESSION TAG SEQADV 6F4R TYR A 179 UNP Q8N371 EXPRESSION TAG SEQADV 6F4R PHE A 180 UNP Q8N371 EXPRESSION TAG SEQADV 6F4R GLN A 181 UNP Q8N371 EXPRESSION TAG SEQADV 6F4R SER A 182 UNP Q8N371 EXPRESSION TAG SEQADV 6F4R ALA A 217 UNP Q8N371 CYS 217 ENGINEERED MUTATION SEQADV 6F4R ALA A 232 UNP Q8N371 CYS 232 ENGINEERED MUTATION SEQADV 6F4R ALA A 295 UNP Q8N371 CYS 295 ENGINEERED MUTATION SEQADV 6F4R CSO A 308 UNP Q8N371 ASN 308 ENGINEERED MUTATION SEQADV 6F4R ALA A 384 UNP Q8N371 CYS 384 ENGINEERED MUTATION SEQRES 1 A 255 HIS HIS HIS HIS HIS HIS SER SER GLY VAL ASP LEU GLY SEQRES 2 A 255 THR GLU ASN LEU TYR PHE GLN SER THR VAL PRO ARG LEU SEQRES 3 A 255 HIS ARG PRO SER LEU GLN HIS PHE ARG GLU GLN PHE LEU SEQRES 4 A 255 VAL PRO GLY ARG PRO VAL ILE LEU LYS GLY VAL ALA ASP SEQRES 5 A 255 HIS TRP PRO ALA MET GLN LYS TRP SER LEU GLU TYR ILE SEQRES 6 A 255 GLN GLU ILE ALA GLY ALA ARG THR VAL PRO VAL GLU VAL SEQRES 7 A 255 GLY SER ARG TYR THR ASP GLU GLU TRP SER GLN THR LEU SEQRES 8 A 255 MET THR VAL ASN GLU PHE ILE SER LYS TYR ILE VAL ASN SEQRES 9 A 255 GLU PRO ARG ASP VAL GLY TYR LEU ALA GLN HIS GLN LEU SEQRES 10 A 255 PHE ASP GLN ILE PRO GLU LEU LYS GLN ASP ILE SER ILE SEQRES 11 A 255 PRO ASP TYR ALA SER LEU GLY ASP GLY GLU GLU GLU GLU SEQRES 12 A 255 ILE THR ILE CSO ALA TRP PHE GLY PRO GLN GLY THR ILE SEQRES 13 A 255 SER PRO LEU HIS GLN ASP PRO GLN GLN ASN PHE LEU VAL SEQRES 14 A 255 GLN VAL MET GLY ARG LYS TYR ILE ARG LEU TYR SER PRO SEQRES 15 A 255 GLN GLU SER GLY ALA LEU TYR PRO HIS ASP THR HIS LEU SEQRES 16 A 255 LEU HIS ASN THR SER GLN VAL ASP VAL GLU ASN PRO ASP SEQRES 17 A 255 LEU GLU LYS PHE PRO LYS PHE ALA LYS ALA PRO PHE LEU SEQRES 18 A 255 SER ALA ILE LEU SER PRO GLY GLU ILE LEU PHE ILE PRO SEQRES 19 A 255 VAL LYS TYR TRP HIS TYR VAL ARG ALA LEU ASP LEU SER SEQRES 20 A 255 PHE SER VAL SER PHE TRP TRP SER SEQRES 1 B 5 CYS ALA ARG ALA TYR HET CSO A 308 17 HET MN A 501 1 HET OGA A 502 13 HET TRS A 503 20 HETNAM CSO S-HYDROXYCYSTEINE HETNAM MN MANGANESE (II) ION HETNAM OGA N-OXALYLGLYCINE HETNAM TRS 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL HETSYN TRS TRIS BUFFER FORMUL 1 CSO C3 H7 N O3 S FORMUL 3 MN MN 2+ FORMUL 4 OGA C4 H5 N O5 FORMUL 5 TRS C4 H12 N O3 1+ FORMUL 6 HOH *360(H2 O) HELIX 1 AA1 SER A 191 PHE A 199 1 9 HELIX 2 AA2 TRP A 215 TRP A 221 1 7 HELIX 3 AA3 SER A 222 GLY A 231 1 10 HELIX 4 AA4 VAL A 255 ILE A 263 1 9 HELIX 5 AA5 GLN A 277 ILE A 282 1 6 HELIX 6 AA6 ILE A 282 GLN A 287 1 6 HELIX 7 AA7 PRO A 292 GLY A 298 5 7 HELIX 8 AA8 GLU A 301 ILE A 305 5 5 HELIX 9 AA9 SER A 342 TYR A 350 5 9 HELIX 10 AB1 PHE A 373 ALA A 379 5 7 SHEET 1 AA1 9 ARG A 186 HIS A 188 0 SHEET 2 AA1 9 VAL A 206 LYS A 209 1 O LYS A 209 N LEU A 187 SHEET 3 AA1 9 ILE A 391 ILE A 394 -1 O PHE A 393 N VAL A 206 SHEET 4 AA1 9 GLN A 326 MET A 333 -1 N LEU A 329 O LEU A 392 SHEET 5 AA1 9 SER A 408 TRP A 415 -1 O VAL A 411 N VAL A 330 SHEET 6 AA1 9 THR A 306 GLY A 312 -1 N GLY A 312 O SER A 408 SHEET 7 AA1 9 GLY A 271 HIS A 276 -1 N HIS A 276 O ALA A 309 SHEET 8 AA1 9 THR A 234 VAL A 239 -1 N GLU A 238 O TYR A 272 SHEET 9 AA1 9 SER A 249 THR A 254 -1 O SER A 249 N VAL A 239 SHEET 1 AA2 4 ILE A 317 HIS A 321 0 SHEET 2 AA2 4 TRP A 399 ALA A 404 -1 O HIS A 400 N HIS A 321 SHEET 3 AA2 4 LYS A 336 TYR A 341 -1 N TYR A 337 O ARG A 403 SHEET 4 AA2 4 LEU A 382 LEU A 386 -1 O LEU A 386 N LYS A 336 SSBOND 1 CSO A 308 CYS B 139 1555 1555 2.01 LINK C ILE A 307 N CSO A 308 1555 1555 1.32 LINK C CSO A 308 N ALA A 309 1555 1555 1.31 LINK NE2 HIS A 321 MN MN A 501 1555 1555 2.22 LINK OD2 ASP A 323 MN MN A 501 1555 1555 2.13 LINK NE2 HIS A 400 MN MN A 501 1555 1555 2.28 LINK MN MN A 501 O2 OGA A 502 1555 1555 2.17 LINK MN MN A 501 O2' OGA A 502 1555 1555 2.19 LINK MN MN A 501 O HOH A 749 1555 1555 2.27 SITE 1 AC1 5 HIS A 321 ASP A 323 HIS A 400 OGA A 502 SITE 2 AC1 5 HOH A 749 SITE 1 AC2 15 TYR A 272 TRP A 310 SER A 318 HIS A 321 SITE 2 AC2 15 ASP A 323 ASN A 327 LEU A 329 LYS A 336 SITE 3 AC2 15 HIS A 400 VAL A 402 SER A 412 TRP A 414 SITE 4 AC2 15 MN A 501 HOH A 615 HOH A 747 SITE 1 AC3 8 LEU A 200 VAL A 201 GLY A 203 GLN A 326 SITE 2 AC3 8 VAL A 396 HOH A 610 HOH A 651 HOH A 693 CRYST1 49.429 64.810 77.982 90.00 90.00 90.00 P 21 21 21 4 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 0.020231 0.000000 0.000000 0.00000 SCALE2 0.000000 0.015430 0.000000 0.00000 SCALE3 0.000000 0.000000 0.012823 0.00000