HEADER OXIDOREDUCTASE/STRUCTURAL PROTEIN 18-JUL-14 4QX7 TITLE CRYSTAL STRUCTURE OF HISTONE DEMETHYLASE KDM2A-H3K36ME2 WITH ALPHA-KG 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: HISTONE H3.2; COMPND 21 CHAIN: E, F; COMPND 22 FRAGMENT: UNP RESIDUES 30-44; COMPND 23 ENGINEERED: YES 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: BL21(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: BL21(DE3); SOURCE 17 MOL_ID: 3; SOURCE 18 SYNTHETIC: YES; SOURCE 19 ORGANISM_SCIENTIFIC: MUS MUSCULUS; SOURCE 20 ORGANISM_COMMON: MOUSE; SOURCE 21 ORGANISM_TAXID: 10090; SOURCE 22 OTHER_DETAILS: METHYLATED H3 PEPTIDE WAS SYNTHESIZED KEYWDS CUPIN SUBFAMILY FE(II)/2-OG DIOXYGENASE, JMJC DOMAIN, HISTONE KEYWDS 2 DEMETHYLASE, OXIDOREDUCTASE-STRUCTURAL PROTEIN COMPLEX EXPDTA X-RAY DIFFRACTION AUTHOR Z.J.CHENG,D.J.PATEL REVDAT 1 05-NOV-14 4QX7 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. 2.34 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.5.0109 REMARK 3 AUTHORS : MURSHUDOV,VAGIN,DODSON REMARK 3 REMARK 3 REFINEMENT TARGET : MAXIMUM LIKELIHOOD REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.34 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 85.47 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 98.8 REMARK 3 NUMBER OF REFLECTIONS : 32531 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 CROSS-VALIDATION METHOD : THROUGHOUT REMARK 3 FREE R VALUE TEST SET SELECTION : RANDOM REMARK 3 R VALUE (WORKING + TEST SET) : 0.203 REMARK 3 R VALUE (WORKING SET) : 0.200 REMARK 3 FREE R VALUE : 0.258 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.000 REMARK 3 FREE R VALUE TEST SET COUNT : 1728 REMARK 3 REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN. REMARK 3 TOTAL NUMBER OF BINS USED : 20 REMARK 3 BIN RESOLUTION RANGE HIGH (A) : 2.34 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.40 REMARK 3 REFLECTION IN BIN (WORKING SET) : 2271 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 96.11 REMARK 3 BIN R VALUE (WORKING SET) : 0.2500 REMARK 3 BIN FREE R VALUE SET COUNT : 127 REMARK 3 BIN FREE R VALUE : 0.3170 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 6706 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 22 REMARK 3 SOLVENT ATOMS : 265 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 36.76 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 0.38000 REMARK 3 B22 (A**2) : 3.11000 REMARK 3 B33 (A**2) : -3.50000 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 ESTIMATED OVERALL COORDINATE ERROR. REMARK 3 ESU BASED ON R VALUE (A): 0.627 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.289 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.221 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 9.256 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.946 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.910 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 6966 ; 0.015 ; 0.022 REMARK 3 BOND LENGTHS OTHERS (A): NULL ; NULL ; NULL REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 9455 ; 1.557 ; 1.952 REMARK 3 BOND ANGLES OTHERS (DEGREES): NULL ; NULL ; NULL REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 825 ; 6.294 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 344 ;37.993 ;24.128 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 1196 ;17.826 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 38 ;23.784 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 1012 ; 0.106 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 5340 ; 0.007 ; 0.021 REMARK 3 GENERAL PLANES OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED CONTACTS OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION OTHERS (A): NULL ; NULL ; NULL REMARK 3 H-BOND (X...Y) REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 H-BOND (X...Y) OTHERS (A): NULL ; NULL ; NULL REMARK 3 POTENTIAL METAL-ION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 POTENTIAL METAL-ION OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY VDW REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY VDW OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY H-BOND REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY H-BOND OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY METAL-ION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY METAL-ION OTHERS (A): NULL ; NULL ; NULL REMARK 3 REMARK 3 ISOTROPIC THERMAL FACTOR RESTRAINTS. COUNT RMS WEIGHT REMARK 3 MAIN-CHAIN BOND REFINED ATOMS (A**2): 4101 ; 0.742 ; 1.500 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 6688 ; 1.468 ; 2.000 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 2865 ; 2.306 ; 3.000 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 2761 ; 3.878 ; 4.500 REMARK 3 SIDE-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 LONG RANGE B REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 LONG RANGE B OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 REMARK 3 ANISOTROPIC THERMAL FACTOR RESTRAINTS. COUNT RMS WEIGHT REMARK 3 RIGID-BOND RESTRAINTS (A**2): NULL ; NULL ; NULL REMARK 3 SPHERICITY; FREE ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SPHERICITY; BONDED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 REMARK 3 NCS RESTRAINTS STATISTICS REMARK 3 NUMBER OF DIFFERENT NCS GROUPS : 1 REMARK 3 REMARK 3 NCS GROUP NUMBER : 1 REMARK 3 CHAIN NAMES : A B REMARK 3 NUMBER OF COMPONENTS NCS GROUP : 2 REMARK 3 COMPONENT C SSSEQI TO C SSSEQI CODE REMARK 3 1 A 36 A 364 2 REMARK 3 1 B 36 B 364 2 REMARK 3 2 A 451 A 516 2 REMARK 3 2 B 451 B 516 2 REMARK 3 GROUP CHAIN COUNT RMS WEIGHT REMARK 3 TIGHT POSITIONAL 1 A (A): 1621 ; 0.07 ; 0.05 REMARK 3 MEDIUM POSITIONAL 1 A (A): 1646 ; 0.07 ; 0.50 REMARK 3 TIGHT THERMAL 1 B (A**2): 1621 ; 0.19 ; 0.50 REMARK 3 MEDIUM THERMAL 1 B (A**2): 1646 ; 0.18 ; 2.00 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : NULL REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : MASK REMARK 3 PARAMETERS FOR MASK CALCULATION REMARK 3 VDW PROBE RADIUS : 1.40 REMARK 3 ION PROBE RADIUS : 0.80 REMARK 3 SHRINKAGE RADIUS : 0.80 REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: HYDROGENS HAVE BEEN ADDED IN THE RIDING REMARK 3 POSITIONS REMARK 4 REMARK 4 4QX7 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 26-AUG-14. REMARK 100 THE RCSB ID CODE IS RCSB086626. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 17-MAR-10 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 5.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : APS REMARK 200 BEAMLINE : 24-ID-C 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 : SI 111 CHANNEL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 315 REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : HKL-2000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 34287 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.340 REMARK 200 RESOLUTION RANGE LOW (A) : 85.470 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 3.240 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 98.8 REMARK 200 DATA REDUNDANCY : 6.500 REMARK 200 R MERGE (I) : 0.10900 REMARK 200 R SYM (I) : 0.10900 REMARK 200 FOR THE DATA SET : NULL REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.35 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.40 REMARK 200 COMPLETENESS FOR SHELL (%) : 97.3 REMARK 200 DATA REDUNDANCY IN SHELL : 4.60 REMARK 200 R MERGE FOR SHELL (I) : 0.41600 REMARK 200 R SYM FOR SHELL (I) : 0.31300 REMARK 200 FOR SHELL : NULL REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: PHASES REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 40.93 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.08 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.15 M NA CITRATE, 18-22% PEG 3350, PH REMARK 280 5.5, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 293K 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 27.17150 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 85.47200 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 43.24350 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 85.47200 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 27.17150 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 43.24350 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: TRIMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: TRIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 6570 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 17640 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -64.0 KCAL/MOL 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 SOFTWARE DETERMINED QUATERNARY STRUCTURE: TRIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 6310 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 17350 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -59.0 KCAL/MOL 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 ARG E 42 REMARK 465 PRO E 43 REMARK 465 ALA F 29 REMARK 465 PRO F 30 REMARK 465 ARG F 40 REMARK 465 TYR F 41 REMARK 465 ARG F 42 REMARK 465 PRO F 43 REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: COVALENT BOND ANGLES 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,A3,1X,A1,I4,A1,3(1X,A4,2X),12X,F5.1) 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 ATM2 ATM3 REMARK 500 ARG A 36 NE - CZ - NH1 ANGL. DEV. = 3.5 DEGREES REMARK 500 ASP A 112 CB - CG - OD1 ANGL. DEV. = 5.8 DEGREES REMARK 500 ASP C 112 CB - CG - OD1 ANGL. DEV. = 5.5 DEGREES REMARK 500 LEU C 201 CA - CB - CG ANGL. DEV. = 14.0 DEGREES 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 GLN A 116 16.20 49.00 REMARK 500 PRO A 194 96.44 -65.25 REMARK 500 ASN A 304 48.88 -147.37 REMARK 500 GLU B 483 -82.42 -77.85 REMARK 500 SER B 501 23.17 -77.77 REMARK 500 GLN C 116 16.15 47.40 REMARK 500 PRO C 194 97.88 -66.91 REMARK 500 ASN C 304 47.42 -146.06 REMARK 500 GLU D 483 -81.24 -74.03 REMARK 500 SER D 501 26.70 -78.32 REMARK 500 MLY F 36 41.47 -97.98 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 NI A 702 NI REMARK 620 N RES CSSEQI ATOM REMARK 620 1 AKG A 701 O5 REMARK 620 2 HIS A 212 NE2 89.1 REMARK 620 3 AKG A 701 O1 71.0 89.8 REMARK 620 4 HIS A 284 NE2 97.1 91.1 168.1 REMARK 620 5 ASP A 214 OD1 165.1 103.6 116.0 75.3 REMARK 620 N 1 2 3 4 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 NI C 702 NI REMARK 620 N RES CSSEQI ATOM REMARK 620 1 AKG C 701 O5 REMARK 620 2 HIS C 212 NE2 98.3 REMARK 620 3 AKG C 701 O1 76.8 88.0 REMARK 620 4 HIS C 284 NE2 91.6 91.3 168.2 REMARK 620 5 ASP C 214 OD1 153.6 104.8 116.2 75.4 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 AKG A 701 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE NI A 702 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE AKG C 701 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE NI C 702 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 4TN7 RELATED DB: PDB REMARK 900 RELATED ID: 2YU1 RELATED DB: PDB REMARK 900 RELATED ID: 2YU2 RELATED DB: PDB REMARK 900 RELATED ID: 4QWN RELATED DB: PDB REMARK 900 RELATED ID: 4QX8 RELATED DB: PDB REMARK 900 RELATED ID: 4QXB RELATED DB: PDB REMARK 900 RELATED ID: 4QXC RELATED DB: PDB REMARK 900 RELATED ID: 4QXH RELATED DB: PDB DBREF 4QX7 A 36 364 UNP F6YRW4 F6YRW4_MOUSE 36 364 DBREF 4QX7 B 450 517 UNP F6YRW4 F6YRW4_MOUSE 450 517 DBREF 4QX7 C 36 364 UNP F6YRW4 F6YRW4_MOUSE 36 364 DBREF 4QX7 D 450 517 UNP F6YRW4 F6YRW4_MOUSE 450 517 DBREF 4QX7 E 29 43 UNP P84228 H32_MOUSE 30 44 DBREF 4QX7 F 29 43 UNP P84228 H32_MOUSE 30 44 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 MLY LYS PRO HIS ARG TYR SEQRES 2 E 15 ARG PRO SEQRES 1 F 15 ALA PRO ALA THR GLY GLY VAL MLY LYS PRO HIS ARG TYR SEQRES 2 F 15 ARG PRO MODRES 4QX7 MLY E 36 LYS N-DIMETHYL-LYSINE MODRES 4QX7 MLY F 36 LYS N-DIMETHYL-LYSINE HET MLY E 36 11 HET MLY F 36 11 HET AKG A 701 10 HET NI A 702 1 HET AKG C 701 10 HET NI C 702 1 HETNAM MLY N-DIMETHYL-LYSINE HETNAM AKG 2-OXOGLUTARIC ACID HETNAM NI NICKEL (II) ION FORMUL 5 MLY 2(C8 H18 N2 O2) FORMUL 7 AKG 2(C5 H6 O5) FORMUL 8 NI 2(NI 2+) FORMUL 11 HOH *265(H2 O) HELIX 1 1 ASP A 39 THR A 46 1 8 HELIX 2 2 GLU A 58 PHE A 62 5 5 HELIX 3 3 ASN A 63 GLY A 71 1 9 HELIX 4 4 THR A 94 GLY A 103 1 10 HELIX 5 5 MET A 123 THR A 132 1 10 HELIX 6 6 PRO A 133 ARG A 137 5 5 HELIX 7 7 THR A 151 VAL A 157 5 7 HELIX 8 8 PRO A 160 ASP A 167 1 8 HELIX 9 9 ASP A 167 TRP A 173 1 7 HELIX 10 10 PRO A 174 GLN A 181 1 8 HELIX 11 11 ASP A 214 THR A 218 5 5 HELIX 12 12 THR A 237 GLY A 251 1 15 HELIX 13 13 PHE A 257 ARG A 261 5 5 HELIX 14 14 ASN A 304 ARG A 319 1 16 HELIX 15 15 PRO A 321 ARG A 325 5 5 HELIX 16 16 PHE A 328 ASN A 346 1 19 HELIX 17 17 THR A 351 GLU A 364 1 14 HELIX 18 18 THR B 454 SER B 470 1 17 HELIX 19 19 PRO B 472 CYS B 477 1 6 HELIX 20 20 ASP B 484 ALA B 500 1 17 HELIX 21 21 ASP C 39 THR C 46 1 8 HELIX 22 22 GLU C 58 PHE C 62 5 5 HELIX 23 23 ASN C 63 GLY C 71 1 9 HELIX 24 24 THR C 94 GLY C 103 1 10 HELIX 25 25 MET C 123 THR C 132 1 10 HELIX 26 26 PRO C 133 ARG C 137 5 5 HELIX 27 27 THR C 151 VAL C 157 5 7 HELIX 28 28 PRO C 160 ASP C 167 1 8 HELIX 29 29 ASP C 167 TRP C 173 1 7 HELIX 30 30 PRO C 174 GLN C 181 1 8 HELIX 31 31 ALA C 187 MET C 191 5 5 HELIX 32 32 ASP C 214 THR C 218 5 5 HELIX 33 33 THR C 237 GLY C 251 1 15 HELIX 34 34 PHE C 257 ARG C 261 5 5 HELIX 35 35 ASN C 304 ARG C 319 1 16 HELIX 36 36 PRO C 321 ARG C 325 5 5 HELIX 37 37 PHE C 328 ASN C 346 1 19 HELIX 38 38 THR C 351 GLU C 364 1 14 HELIX 39 39 THR D 454 SER D 470 1 17 HELIX 40 40 PRO D 472 LYS D 476 5 5 HELIX 41 41 ASP D 484 ALA D 500 1 17 SHEET 1 A 9 THR A 55 PHE A 56 0 SHEET 2 A 9 LEU A 76 PHE A 78 1 O ILE A 77 N THR A 55 SHEET 3 A 9 THR A 275 ILE A 278 -1 O THR A 275 N PHE A 78 SHEET 4 A 9 SER A 219 GLN A 226 -1 N VAL A 220 O ILE A 278 SHEET 5 A 9 THR A 292 PHE A 299 -1 O PHE A 295 N HIS A 223 SHEET 6 A 9 TYR A 199 SER A 203 -1 N SER A 203 O THR A 292 SHEET 7 A 9 TYR A 141 GLU A 147 -1 N VAL A 143 O MET A 202 SHEET 8 A 9 MET A 107 ASP A 112 -1 N MET A 111 O ASN A 142 SHEET 9 A 9 GLY A 118 THR A 122 -1 O ILE A 119 N VAL A 110 SHEET 1 B 4 CYS A 207 HIS A 212 0 SHEET 2 B 4 ILE A 283 THR A 288 -1 O VAL A 286 N THR A 209 SHEET 3 B 4 LYS A 229 ILE A 234 -1 N VAL A 230 O TYR A 287 SHEET 4 B 4 GLN A 266 LEU A 270 -1 O LEU A 270 N LYS A 229 SHEET 1 C 9 THR C 55 PHE C 56 0 SHEET 2 C 9 LEU C 76 PHE C 78 1 O ILE C 77 N THR C 55 SHEET 3 C 9 THR C 275 ILE C 278 -1 O THR C 275 N PHE C 78 SHEET 4 C 9 SER C 219 GLN C 226 -1 N VAL C 220 O ILE C 278 SHEET 5 C 9 THR C 292 PHE C 299 -1 O PHE C 295 N HIS C 223 SHEET 6 C 9 TYR C 199 SER C 203 -1 N SER C 203 O THR C 292 SHEET 7 C 9 TYR C 141 GLU C 147 -1 N VAL C 143 O MET C 202 SHEET 8 C 9 MET C 107 ASP C 112 -1 N MET C 111 O ASN C 142 SHEET 9 C 9 LYS C 117 THR C 122 -1 O ILE C 119 N VAL C 110 SHEET 1 D 4 CYS C 207 HIS C 212 0 SHEET 2 D 4 ILE C 283 THR C 288 -1 O VAL C 286 N THR C 209 SHEET 3 D 4 LYS C 229 ILE C 234 -1 N VAL C 230 O TYR C 287 SHEET 4 D 4 GLN C 266 LEU C 270 -1 O LEU C 270 N LYS C 229 LINK C VAL E 35 N MLY E 36 1555 1555 1.34 LINK C MLY E 36 N LYS E 37 1555 1555 1.34 LINK C VAL F 35 N MLY F 36 1555 1555 1.34 LINK C MLY F 36 N LYS F 37 1555 1555 1.33 LINK O5 AKG A 701 NI NI A 702 1555 1555 2.13 LINK O5 AKG C 701 NI NI C 702 1555 1555 2.16 LINK NE2 HIS A 212 NI NI A 702 1555 1555 2.19 LINK NE2 HIS C 212 NI NI C 702 1555 1555 2.19 LINK O1 AKG C 701 NI NI C 702 1555 1555 2.29 LINK NE2 HIS C 284 NI NI C 702 1555 1555 2.34 LINK O1 AKG A 701 NI NI A 702 1555 1555 2.36 LINK NE2 HIS A 284 NI NI A 702 1555 1555 2.38 LINK OD1 ASP A 214 NI NI A 702 1555 1555 2.47 LINK OD1 ASP C 214 NI NI C 702 1555 1555 2.49 SITE 1 AC1 14 ASN A 142 ILE A 144 LEU A 201 THR A 209 SITE 2 AC1 14 HIS A 212 ASP A 214 TYR A 222 LYS A 229 SITE 3 AC1 14 HIS A 284 VAL A 286 NI A 702 HOH A 819 SITE 4 AC1 14 HOH A 832 MLY E 36 SITE 1 AC2 5 HIS A 212 ASP A 214 TYR A 222 HIS A 284 SITE 2 AC2 5 AKG A 701 SITE 1 AC3 13 ASN C 142 ILE C 144 LEU C 201 THR C 209 SITE 2 AC3 13 HIS C 212 ASP C 214 TYR C 222 LYS C 229 SITE 3 AC3 13 HIS C 284 VAL C 286 NI C 702 HOH C 818 SITE 4 AC3 13 MLY F 36 SITE 1 AC4 4 HIS C 212 ASP C 214 HIS C 284 AKG C 701 CRYST1 54.343 86.487 170.944 90.00 90.00 90.00 P 21 21 21 8 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 0.018402 0.000000 0.000000 0.00000 SCALE2 0.000000 0.011562 0.000000 0.00000 SCALE3 0.000000 0.000000 0.005850 0.00000