HEADER OXIDOREDUCTASE 03-JUN-14 4TN7 TITLE CRYSTAL STRUCTURE OF MOUSE KDM2A-H3K36ME-NO COMPLEX COMPND MOL_ID: 1; COMPND 2 MOLECULE: LYSINE-SPECIFIC DEMETHYLASE 2A; COMPND 3 CHAIN: A, C; COMPND 4 FRAGMENT: UNP RESIDUES 36-364; COMPND 5 SYNONYM: F-BOX AND LEUCINE-RICH REPEAT PROTEIN 11,F-BOX/LRR-REPEAT COMPND 6 PROTEIN 11,JMJC DOMAIN-CONTAINING HISTONE DEMETHYLATION PROTEIN 1A, COMPND 7 [HISTONE-H3]-LYSINE-36 DEMETHYLASE 1A; COMPND 8 EC: 1.14.11.27; COMPND 9 ENGINEERED: YES; COMPND 10 MOL_ID: 2; COMPND 11 MOLECULE: LYSINE-SPECIFIC DEMETHYLASE 2A; COMPND 12 CHAIN: B, D; COMPND 13 FRAGMENT: UNP RESIDUES 450-517; COMPND 14 SYNONYM: F-BOX AND LEUCINE-RICH REPEAT PROTEIN 11,F-BOX/LRR-REPEAT COMPND 15 PROTEIN 11,JMJC DOMAIN-CONTAINING HISTONE DEMETHYLATION PROTEIN 1A, COMPND 16 [HISTONE-H3]-LYSINE-36 DEMETHYLASE 1A; COMPND 17 EC: 1.14.11.27; COMPND 18 ENGINEERED: YES; COMPND 19 MOL_ID: 3; COMPND 20 MOLECULE: PEPTIDE; COMPND 21 CHAIN: E, F; COMPND 22 ENGINEERED: YES; COMPND 23 OTHER_DETAILS: CHEMICALLY SYNTHESIZED PEPTIDE SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: MUS MUSCULUS; SOURCE 3 ORGANISM_COMMON: MOUSE; SOURCE 4 ORGANISM_TAXID: 10090; SOURCE 5 GENE: KDM2A, FBXL11, JHDM1A, KIAA1004; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 8 EXPRESSION_SYSTEM_STRAIN: BL(DE3); SOURCE 9 MOL_ID: 2; SOURCE 10 ORGANISM_SCIENTIFIC: MUS MUSCULUS; SOURCE 11 ORGANISM_COMMON: MOUSE; SOURCE 12 ORGANISM_TAXID: 10090; SOURCE 13 GENE: KDM2A, FBXL11, JHDM1A, KIAA1004; SOURCE 14 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 15 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 16 EXPRESSION_SYSTEM_STRAIN: BL(DE3); SOURCE 17 MOL_ID: 3; SOURCE 18 SYNTHETIC: YES; SOURCE 19 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 20 ORGANISM_COMMON: HUMAN; SOURCE 21 ORGANISM_TAXID: 9606 KEYWDS OXIDOREDUCTASE EXPDTA X-RAY DIFFRACTION AUTHOR Z.CHENG REVDAT 4 27-SEP-23 4TN7 1 REMARK LINK REVDAT 3 25-DEC-19 4TN7 1 REMARK REVDAT 2 20-SEP-17 4TN7 1 HEADER SOURCE JRNL REMARK REVDAT 1 13-MAY-15 4TN7 0 JRNL AUTH Z.CHENG,P.CHEUNG,A.J.KUO,E.T.YUKL,C.M.WILMOT,O.GOZANI, JRNL AUTH 2 D.J.PATEL JRNL TITL A MOLECULAR THREADING MECHANISM UNDERLIES JUMONJI LYSINE JRNL TITL 2 DEMETHYLASE KDM2A REGULATION OF METHYLATED H3K36. JRNL REF GENES DEV. V. 28 1758 2014 JRNL REFN ISSN 0890-9369 JRNL PMID 25128496 JRNL DOI 10.1101/GAD.246561.114 REMARK 2 REMARK 2 RESOLUTION. 2.20 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX (PHENIX.REFINE: DEV_1760) 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) : 2.20 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 45.17 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.430 REMARK 3 COMPLETENESS FOR RANGE (%) : 97.6 REMARK 3 NUMBER OF REFLECTIONS : 40864 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.232 REMARK 3 R VALUE (WORKING SET) : 0.229 REMARK 3 FREE R VALUE : 0.279 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.060 REMARK 3 FREE R VALUE TEST SET COUNT : 2067 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 45.1757 - 5.4306 0.98 2620 148 0.2244 0.2600 REMARK 3 2 5.4306 - 4.3115 0.98 2612 139 0.2038 0.2372 REMARK 3 3 4.3115 - 3.7668 0.98 2625 138 0.1986 0.2354 REMARK 3 4 3.7668 - 3.4225 0.98 2604 129 0.2023 0.2385 REMARK 3 5 3.4225 - 3.1773 0.97 2586 149 0.2260 0.2846 REMARK 3 6 3.1773 - 2.9900 0.98 2608 140 0.2365 0.3163 REMARK 3 7 2.9900 - 2.8403 0.98 2564 136 0.2440 0.3128 REMARK 3 8 2.8403 - 2.7167 0.98 2581 130 0.2421 0.2822 REMARK 3 9 2.7167 - 2.6121 0.98 2584 146 0.2498 0.3029 REMARK 3 10 2.6121 - 2.5220 0.98 2637 126 0.2500 0.3366 REMARK 3 11 2.5220 - 2.4431 0.98 2571 133 0.2526 0.3075 REMARK 3 12 2.4431 - 2.3733 0.98 2608 155 0.2729 0.3424 REMARK 3 13 2.3733 - 2.3108 0.98 2596 136 0.2694 0.3296 REMARK 3 14 2.3108 - 2.2544 0.98 2634 124 0.2719 0.3177 REMARK 3 15 2.2544 - 2.2000 0.93 2367 138 0.2779 0.3313 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) : 0.310 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 28.340 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : NULL 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 : 0.002 6873 REMARK 3 ANGLE : 0.532 9314 REMARK 3 CHIRALITY : 0.022 1000 REMARK 3 PLANARITY : 0.002 1194 REMARK 3 DIHEDRAL : 13.111 2558 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): 13.8096 -1.0164 10.9226 REMARK 3 T TENSOR REMARK 3 T11: 0.2097 T22: 0.2252 REMARK 3 T33: 0.1910 T12: 0.0113 REMARK 3 T13: -0.0055 T23: 0.0119 REMARK 3 L TENSOR REMARK 3 L11: 0.0586 L22: 0.4660 REMARK 3 L33: -0.0330 L12: -0.1748 REMARK 3 L13: -0.1084 L23: 0.1921 REMARK 3 S TENSOR REMARK 3 S11: -0.0151 S12: 0.0075 S13: 0.0036 REMARK 3 S21: 0.0141 S22: 0.0055 S23: 0.0292 REMARK 3 S31: -0.0050 S32: -0.0072 S33: 0.0017 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 4TN7 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 02-JAN-15. REMARK 100 THE DEPOSITION ID IS D_1000201908. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 12-FEB-12 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : NULL REMARK 200 NUMBER OF CRYSTALS USED : NULL REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : APS REMARK 200 BEAMLINE : 24-ID-E REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.979 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 315 REMARK 200 INTENSITY-INTEGRATION SOFTWARE : NULL REMARK 200 DATA SCALING SOFTWARE : NULL REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 40902 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.200 REMARK 200 RESOLUTION RANGE LOW (A) : 50.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 97.9 REMARK 200 DATA REDUNDANCY : 2.900 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 9.1000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.20 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.25 REMARK 200 COMPLETENESS FOR SHELL (%) : 97.5 REMARK 200 DATA REDUNDANCY IN SHELL : 2.80 REMARK 200 R MERGE FOR SHELL (I) : 0.48200 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 1.800 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: NULL REMARK 200 STARTING MODEL: 2YU1 REMARK 200 REMARK 200 REMARK: PLATE-LIKE CRYSTALS REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 44.77 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.23 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 100 MM LI-CITRATE 18-30% PEG 3350, REMARK 280 VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 293K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 1 21 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,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 0.00000 REMARK 290 SMTRY2 2 0.000000 1.000000 0.000000 78.96400 REMARK 290 SMTRY3 2 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: TRIMERIC REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, B, E 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: TRIMERIC REMARK 350 APPLY THE FOLLOWING TO CHAINS: C, D, 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 HIS E 39 REMARK 465 ARG E 40 REMARK 465 TYR E 41 REMARK 465 ARG E 42 REMARK 465 PRO E 43 REMARK 465 HIS F 39 REMARK 465 ARG F 40 REMARK 465 TYR F 41 REMARK 465 ARG F 42 REMARK 465 PRO F 43 REMARK 480 REMARK 480 ZERO OCCUPANCY ATOM REMARK 480 THE FOLLOWING RESIDUES HAVE ATOMS MODELED WITH ZERO REMARK 480 OCCUPANCY. THE LOCATION AND PROPERTIES OF THESE ATOMS REMARK 480 MAY NOT BE RELIABLE. (M=MODEL NUMBER; RES=RESIDUE NAME; REMARK 480 C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE): REMARK 480 M RES C SSEQI ATOMS REMARK 480 ASP A 316 CG REMARK 480 HIS B 455 CG CE1 REMARK 480 HIS D 455 CG 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 ASN A 186 37.09 -96.45 REMARK 500 PRO A 194 88.72 -57.22 REMARK 500 VAL A 196 24.51 -143.52 REMARK 500 LYS A 252 49.62 -92.90 REMARK 500 ASN A 304 50.80 -161.30 REMARK 500 GLU B 483 -71.58 -90.63 REMARK 500 SER B 501 41.58 -109.37 REMARK 500 ASN C 186 33.96 -96.67 REMARK 500 PRO C 194 86.97 -55.82 REMARK 500 VAL C 196 29.30 -142.10 REMARK 500 LYS C 252 45.62 -77.25 REMARK 500 ASN C 304 53.19 -161.93 REMARK 500 VAL D 451 115.90 52.62 REMARK 500 GLU D 483 -75.90 -90.31 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 C 814 DISTANCE = 6.79 ANGSTROMS REMARK 525 HOH C 853 DISTANCE = 8.49 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 FE A 601 FE REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HIS A 212 NE2 REMARK 620 2 ASP A 214 OD1 92.2 REMARK 620 3 HIS A 284 NE2 89.1 88.3 REMARK 620 4 NO A 602 N 87.6 96.6 174.2 REMARK 620 5 SIN A 603 O4 93.0 174.5 90.0 85.5 REMARK 620 N 1 2 3 4 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 FE C 601 FE REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HIS C 212 NE2 REMARK 620 2 ASP C 214 OD1 97.6 REMARK 620 3 HIS C 284 NE2 90.7 81.7 REMARK 620 4 SIN C 602 O2 76.6 171.5 91.9 REMARK 620 5 SIN C 602 O1 122.2 135.4 114.1 52.6 REMARK 620 N 1 2 3 4 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue FE A 601 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue NO A 602 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue SIN A 603 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue FE C 601 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue SIN C 602 DBREF 4TN7 A 36 364 UNP P59997 KDM2A_MOUSE 36 364 DBREF 4TN7 B 450 517 UNP P59997 KDM2A_MOUSE 450 517 DBREF 4TN7 C 36 364 UNP P59997 KDM2A_MOUSE 36 364 DBREF 4TN7 D 450 517 UNP P59997 KDM2A_MOUSE 450 517 DBREF 4TN7 E 29 43 PDB 4TN7 4TN7 29 43 DBREF 4TN7 F 29 43 PDB 4TN7 4TN7 29 43 SEQADV 4TN7 ARG A 159 UNP P59997 TRP 159 CONFLICT SEQADV 4TN7 MET A 202 UNP P59997 ILE 202 CONFLICT SEQADV 4TN7 ARG C 159 UNP P59997 TRP 159 CONFLICT SEQADV 4TN7 MET C 202 UNP P59997 ILE 202 CONFLICT SEQRES 1 A 329 ARG THR PHE ASP LEU GLU GLU LYS LEU GLN THR ASN LYS SEQRES 2 A 329 TYR ASN ALA ASN PHE VAL THR PHE MET GLU GLY LYS ASP SEQRES 3 A 329 PHE ASN VAL GLU TYR ILE GLN ARG GLY GLY LEU ARG ASP SEQRES 4 A 329 PRO LEU ILE PHE LYS ASN SER ASP GLY LEU GLY ILE LYS SEQRES 5 A 329 MET PRO ASP PRO ASP PHE THR VAL ASN ASP VAL LYS MET SEQRES 6 A 329 CYS VAL GLY SER ARG ARG MET VAL ASP VAL MET ASP VAL SEQRES 7 A 329 ASN THR GLN LYS GLY ILE GLU MET THR MET ALA GLN TRP SEQRES 8 A 329 THR ARG TYR TYR GLU THR PRO GLU GLU GLU ARG GLU LYS SEQRES 9 A 329 LEU TYR ASN VAL ILE SER LEU GLU PHE SER HIS THR ARG SEQRES 10 A 329 LEU GLU ASN MET VAL GLN ARG PRO SER THR VAL ASP PHE SEQRES 11 A 329 ILE ASP TRP VAL ASP ASN MET TRP PRO ARG HIS LEU LYS SEQRES 12 A 329 GLU SER GLN THR GLU SER THR ASN ALA ILE LEU GLU MET SEQRES 13 A 329 GLN TYR PRO LYS VAL GLN LYS TYR CYS LEU MET SER VAL SEQRES 14 A 329 ARG GLY CYS TYR THR ASP PHE HIS VAL ASP PHE GLY GLY SEQRES 15 A 329 THR SER VAL TRP TYR HIS ILE HIS GLN GLY GLY LYS VAL SEQRES 16 A 329 PHE TRP LEU ILE PRO PRO THR ALA HIS ASN LEU GLU LEU SEQRES 17 A 329 TYR GLU ASN TRP LEU LEU SER GLY LYS GLN GLY ASP ILE SEQRES 18 A 329 PHE LEU GLY ASP ARG VAL SER ASP CYS GLN ARG ILE GLU SEQRES 19 A 329 LEU LYS GLN GLY TYR THR PHE VAL ILE PRO SER GLY TRP SEQRES 20 A 329 ILE HIS ALA VAL TYR THR PRO THR ASP THR LEU VAL PHE SEQRES 21 A 329 GLY GLY ASN PHE LEU HIS SER PHE ASN ILE PRO MET GLN SEQRES 22 A 329 LEU LYS ILE TYR SER ILE GLU ASP ARG THR ARG VAL PRO SEQRES 23 A 329 ASN LYS PHE ARG TYR PRO PHE TYR TYR GLU MET CYS TRP SEQRES 24 A 329 TYR VAL LEU GLU ARG TYR VAL TYR CYS ILE THR ASN ARG SEQRES 25 A 329 SER HIS LEU THR LYS ASP PHE GLN LYS GLU SER LEU SER SEQRES 26 A 329 MET ASP MET GLU SEQRES 1 B 68 GLN VAL HIS LEU THR HIS PHE GLU LEU GLU GLY LEU ARG SEQRES 2 B 68 CYS LEU VAL ASP LYS LEU GLU SER LEU PRO LEU HIS LYS SEQRES 3 B 68 LYS CYS VAL PRO THR GLY ILE GLU ASP GLU ASP ALA LEU SEQRES 4 B 68 ILE ALA ASP VAL LYS ILE LEU LEU GLU GLU LEU ALA SER SEQRES 5 B 68 SER ASP PRO LYS LEU ALA LEU THR GLY VAL PRO ILE VAL SEQRES 6 B 68 GLN TRP PRO SEQRES 1 C 329 ARG THR PHE ASP LEU GLU GLU LYS LEU GLN THR ASN LYS SEQRES 2 C 329 TYR ASN ALA ASN PHE VAL THR PHE MET GLU GLY LYS ASP SEQRES 3 C 329 PHE ASN VAL GLU TYR ILE GLN ARG GLY GLY LEU ARG ASP SEQRES 4 C 329 PRO LEU ILE PHE LYS ASN SER ASP GLY LEU GLY ILE LYS SEQRES 5 C 329 MET PRO ASP PRO ASP PHE THR VAL ASN ASP VAL LYS MET SEQRES 6 C 329 CYS VAL GLY SER ARG ARG MET VAL ASP VAL MET ASP VAL SEQRES 7 C 329 ASN THR GLN LYS GLY ILE GLU MET THR MET ALA GLN TRP SEQRES 8 C 329 THR ARG TYR TYR GLU THR PRO GLU GLU GLU ARG GLU LYS SEQRES 9 C 329 LEU TYR ASN VAL ILE SER LEU GLU PHE SER HIS THR ARG SEQRES 10 C 329 LEU GLU ASN MET VAL GLN ARG PRO SER THR VAL ASP PHE SEQRES 11 C 329 ILE ASP TRP VAL ASP ASN MET TRP PRO ARG HIS LEU LYS SEQRES 12 C 329 GLU SER GLN THR GLU SER THR ASN ALA ILE LEU GLU MET SEQRES 13 C 329 GLN TYR PRO LYS VAL GLN LYS TYR CYS LEU MET SER VAL SEQRES 14 C 329 ARG GLY CYS TYR THR ASP PHE HIS VAL ASP PHE GLY GLY SEQRES 15 C 329 THR SER VAL TRP TYR HIS ILE HIS GLN GLY GLY LYS VAL SEQRES 16 C 329 PHE TRP LEU ILE PRO PRO THR ALA HIS ASN LEU GLU LEU SEQRES 17 C 329 TYR GLU ASN TRP LEU LEU SER GLY LYS GLN GLY ASP ILE SEQRES 18 C 329 PHE LEU GLY ASP ARG VAL SER ASP CYS GLN ARG ILE GLU SEQRES 19 C 329 LEU LYS GLN GLY TYR THR PHE VAL ILE PRO SER GLY TRP SEQRES 20 C 329 ILE HIS ALA VAL TYR THR PRO THR ASP THR LEU VAL PHE SEQRES 21 C 329 GLY GLY ASN PHE LEU HIS SER PHE ASN ILE PRO MET GLN SEQRES 22 C 329 LEU LYS ILE TYR SER ILE GLU ASP ARG THR ARG VAL PRO SEQRES 23 C 329 ASN LYS PHE ARG TYR PRO PHE TYR TYR GLU MET CYS TRP SEQRES 24 C 329 TYR VAL LEU GLU ARG TYR VAL TYR CYS ILE THR ASN ARG SEQRES 25 C 329 SER HIS LEU THR LYS ASP PHE GLN LYS GLU SER LEU SER SEQRES 26 C 329 MET ASP MET GLU SEQRES 1 D 68 GLN VAL HIS LEU THR HIS PHE GLU LEU GLU GLY LEU ARG SEQRES 2 D 68 CYS LEU VAL ASP LYS LEU GLU SER LEU PRO LEU HIS LYS SEQRES 3 D 68 LYS CYS VAL PRO THR GLY ILE GLU ASP GLU ASP ALA LEU SEQRES 4 D 68 ILE ALA ASP VAL LYS ILE LEU LEU GLU GLU LEU ALA SER SEQRES 5 D 68 SER ASP PRO LYS LEU ALA LEU THR GLY VAL PRO ILE VAL SEQRES 6 D 68 GLN TRP PRO SEQRES 1 E 15 ALA PRO ALA THR GLY GLY VAL MLZ LYS PRO HIS ARG TYR SEQRES 2 E 15 ARG PRO SEQRES 1 F 15 ALA PRO ALA THR GLY GLY VAL MLZ LYS PRO HIS ARG TYR SEQRES 2 F 15 ARG PRO HET MLZ E 36 10 HET MLZ F 36 10 HET FE A 601 1 HET NO A 602 2 HET SIN A 603 12 HET FE C 601 1 HET SIN C 602 12 HETNAM MLZ N-METHYL-LYSINE HETNAM FE FE (III) ION HETNAM NO NITRIC OXIDE HETNAM SIN SUCCINIC ACID HETSYN NO NITROGEN MONOXIDE FORMUL 5 MLZ 2(C7 H16 N2 O2) FORMUL 7 FE 2(FE 3+) FORMUL 8 NO N O FORMUL 9 SIN 2(C4 H6 O4) FORMUL 12 HOH *404(H2 O) HELIX 1 AA1 ASP A 39 THR A 46 1 8 HELIX 2 AA2 GLU A 58 PHE A 62 5 5 HELIX 3 AA3 ASN A 63 GLY A 71 1 9 HELIX 4 AA4 THR A 94 GLY A 103 1 10 HELIX 5 AA5 MET A 123 GLU A 131 1 9 HELIX 6 AA6 LEU A 153 VAL A 157 5 5 HELIX 7 AA7 PRO A 160 ASP A 167 1 8 HELIX 8 AA8 ASP A 167 MET A 172 1 6 HELIX 9 AA9 PRO A 174 GLU A 179 1 6 HELIX 10 AB1 ASP A 214 THR A 218 5 5 HELIX 11 AB2 THR A 237 GLY A 251 1 15 HELIX 12 AB3 PHE A 257 VAL A 262 5 6 HELIX 13 AB4 ASN A 304 THR A 318 1 15 HELIX 14 AB5 PRO A 321 ARG A 325 5 5 HELIX 15 AB6 PHE A 328 ASN A 346 1 19 HELIX 16 AB7 THR A 351 MET A 363 1 13 HELIX 17 AB8 THR B 454 SER B 470 1 17 HELIX 18 AB9 PRO B 472 CYS B 477 1 6 HELIX 19 AC1 ASP B 484 LEU B 499 1 16 HELIX 20 AC2 ASP B 503 LEU B 508 1 6 HELIX 21 AC3 ASP C 39 THR C 46 1 8 HELIX 22 AC4 GLU C 58 PHE C 62 5 5 HELIX 23 AC5 ASN C 63 GLY C 71 1 9 HELIX 24 AC6 THR C 94 GLY C 103 1 10 HELIX 25 AC7 MET C 123 THR C 132 1 10 HELIX 26 AC8 LEU C 153 VAL C 157 5 5 HELIX 27 AC9 PRO C 160 ASP C 167 1 8 HELIX 28 AD1 ASP C 167 MET C 172 1 6 HELIX 29 AD2 PRO C 174 GLU C 179 1 6 HELIX 30 AD3 ASP C 214 THR C 218 5 5 HELIX 31 AD4 THR C 237 GLY C 251 1 15 HELIX 32 AD5 LYS C 252 ASP C 255 5 4 HELIX 33 AD6 ASN C 304 THR C 318 1 15 HELIX 34 AD7 PRO C 321 ARG C 325 5 5 HELIX 35 AD8 PHE C 328 ASN C 346 1 19 HELIX 36 AD9 THR C 351 MET C 363 1 13 HELIX 37 AE1 THR D 454 SER D 470 1 17 HELIX 38 AE2 PRO D 472 CYS D 477 1 6 HELIX 39 AE3 ASP D 484 LEU D 499 1 16 HELIX 40 AE4 ASP D 503 LEU D 508 1 6 SHEET 1 AA1 9 THR A 55 PHE A 56 0 SHEET 2 AA1 9 LEU A 76 PHE A 78 1 O ILE A 77 N THR A 55 SHEET 3 AA1 9 THR A 275 ILE A 278 -1 O VAL A 277 N LEU A 76 SHEET 4 AA1 9 SER A 219 GLN A 226 -1 N TYR A 222 O PHE A 276 SHEET 5 AA1 9 THR A 292 PHE A 299 -1 O LEU A 293 N GLN A 226 SHEET 6 AA1 9 TYR A 199 SER A 203 -1 N TYR A 199 O GLY A 296 SHEET 7 AA1 9 TYR A 141 GLU A 147 -1 N LEU A 146 O CYS A 200 SHEET 8 AA1 9 MET A 107 ASP A 112 -1 N MET A 111 O ASN A 142 SHEET 9 AA1 9 GLY A 118 THR A 122 -1 O ILE A 119 N VAL A 110 SHEET 1 AA2 4 TYR A 208 HIS A 212 0 SHEET 2 AA2 4 ILE A 283 TYR A 287 -1 O VAL A 286 N THR A 209 SHEET 3 AA2 4 LYS A 229 ILE A 234 -1 N TRP A 232 O ALA A 285 SHEET 4 AA2 4 GLN A 266 LEU A 270 -1 O LEU A 270 N LYS A 229 SHEET 1 AA3 9 THR C 55 PHE C 56 0 SHEET 2 AA3 9 LEU C 76 PHE C 78 1 O ILE C 77 N THR C 55 SHEET 3 AA3 9 THR C 275 ILE C 278 -1 O VAL C 277 N LEU C 76 SHEET 4 AA3 9 SER C 219 GLN C 226 -1 N TYR C 222 O PHE C 276 SHEET 5 AA3 9 THR C 292 PHE C 299 -1 O LEU C 293 N GLN C 226 SHEET 6 AA3 9 TYR C 199 SER C 203 -1 N TYR C 199 O GLY C 296 SHEET 7 AA3 9 TYR C 141 GLU C 147 -1 N LEU C 146 O CYS C 200 SHEET 8 AA3 9 MET C 107 ASP C 112 -1 N MET C 111 O ASN C 142 SHEET 9 AA3 9 LYS C 117 THR C 122 -1 O ILE C 119 N VAL C 110 SHEET 1 AA4 4 TYR C 208 HIS C 212 0 SHEET 2 AA4 4 ILE C 283 TYR C 287 -1 O VAL C 286 N THR C 209 SHEET 3 AA4 4 LYS C 229 ILE C 234 -1 N TRP C 232 O ALA C 285 SHEET 4 AA4 4 GLN C 266 LEU C 270 -1 O LEU C 270 N LYS C 229 LINK C VAL E 35 N MLZ E 36 1555 1555 1.33 LINK C MLZ E 36 N LYS E 37 1555 1555 1.33 LINK C VAL F 35 N MLZ F 36 1555 1555 1.33 LINK C MLZ F 36 N LYS F 37 1555 1555 1.33 LINK NE2 HIS A 212 FE FE A 601 1555 1555 2.30 LINK OD1 ASP A 214 FE FE A 601 1555 1555 2.21 LINK NE2 HIS A 284 FE FE A 601 1555 1555 2.32 LINK FE FE A 601 N NO A 602 1555 1555 2.06 LINK FE FE A 601 O4 SIN A 603 1555 1555 2.32 LINK NE2 HIS C 212 FE FE C 601 1555 1555 2.54 LINK OD1 ASP C 214 FE FE C 601 1555 1555 2.25 LINK NE2 HIS C 284 FE FE C 601 1555 1555 2.33 LINK FE FE C 601 O2 SIN C 602 1555 1555 2.35 LINK FE FE C 601 O1 SIN C 602 1555 1555 2.50 SITE 1 AC1 5 HIS A 212 ASP A 214 HIS A 284 NO A 602 SITE 2 AC1 5 SIN A 603 SITE 1 AC2 5 HIS A 212 ASP A 214 FE A 601 SIN A 603 SITE 2 AC2 5 MLZ E 36 SITE 1 AC3 10 ASN A 142 THR A 209 HIS A 212 TYR A 222 SITE 2 AC3 10 LYS A 229 HIS A 284 VAL A 286 FE A 601 SITE 3 AC3 10 NO A 602 MLZ E 36 SITE 1 AC4 4 HIS C 212 ASP C 214 HIS C 284 SIN C 602 SITE 1 AC5 10 ASN C 142 ILE C 144 THR C 209 HIS C 212 SITE 2 AC5 10 TYR C 222 LYS C 229 HIS C 284 VAL C 286 SITE 3 AC5 10 FE C 601 MLZ F 36 CRYST1 55.063 157.928 48.706 90.00 90.00 90.00 P 1 21 1 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 0.018161 0.000000 -0.000001 0.00000 SCALE2 0.000000 0.006332 0.000000 0.00000 SCALE3 0.000000 0.000000 0.020531 0.00000