HEADER TRANSFERASE 28-MAR-09 3A1B TITLE CRYSTAL STRUCTURE OF THE DNMT3A ADD DOMAIN IN COMPLEX WITH HISTONE H3 COMPND MOL_ID: 1; COMPND 2 MOLECULE: DNA (CYTOSINE-5)-METHYLTRANSFERASE 3A, HISTONE H3.1; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: ADD(ATRX-DNMT3-DNMT3L) DOMAIN(RESIDUES 476-614), UNP COMPND 5 RESIDUES 2-21(HISTONE H3.1); COMPND 6 SYNONYM: DNMT3A, DNA METHYLTRANSFERASE HSAIIIA, DNA MTASE HSAIIIA, COMPND 7 M.HSAIIIA, H3/A, H3/B, H3/C, H3/D, H3/F, H3/H, H3/I, H3/J, H3/K, COMPND 8 H3/L; COMPND 9 EC: 2.1.1.37; COMPND 10 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 3 ORGANISM_COMMON: HUMAN; SOURCE 4 ORGANISM_TAXID: 9606; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 6 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 7 EXPRESSION_SYSTEM_STRAIN: BL21(DE3); SOURCE 8 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 9 EXPRESSION_SYSTEM_PLASMID: PGEX KEYWDS ZINC-FINGER, HISTONE BINDING, CHROMOSOMAL PROTEIN, DNA DAMAGE, DNA KEYWDS 2 REPAIR, DNA-BINDING, METHYLATION, NUCLEOSOME CORE, NUCLEUS, KEYWDS 3 PHOSPHOPROTEIN, ALTERNATIVE PROMOTER USAGE, METAL-BINDING, KEYWDS 4 METHYLTRANSFERASE, S-ADENOSYL-L-METHIONINE, TRANSFERASE EXPDTA X-RAY DIFFRACTION AUTHOR J.OTANI,K.ARITA,M.ARIYOSHI,M.SHIRAKAWA REVDAT 4 01-NOV-23 3A1B 1 REMARK LINK REVDAT 3 09-AUG-17 3A1B 1 SOURCE REMARK REVDAT 2 13-JUL-11 3A1B 1 VERSN REVDAT 1 10-NOV-09 3A1B 0 JRNL AUTH J.OTANI,T.NANKUMO,K.ARITA,S.INAMOTO,M.ARIYOSHI,M.SHIRAKAWA JRNL TITL STRUCTURAL BASIS FOR RECOGNITION OF H3K4 METHYLATION STATUS JRNL TITL 2 BY THE DNA METHYLTRANSFERASE 3A ATRX-DNMT3-DNMT3L DOMAIN JRNL REF EMBO REP. V. 10 1235 2009 JRNL REFN ISSN 1469-221X JRNL PMID 19834512 JRNL DOI 10.1038/EMBOR.2009.218 REMARK 2 REMARK 2 RESOLUTION. 2.29 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.2.0019 REMARK 3 AUTHORS : MURSHUDOV,SKUBAK,LEBEDEV,PANNU,STEINER, REMARK 3 : NICHOLLS,WINN,LONG,VAGIN REMARK 3 REMARK 3 REFINEMENT TARGET : MAXIMUM LIKELIHOOD REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.29 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 32.72 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 98.1 REMARK 3 NUMBER OF REFLECTIONS : 11534 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) : 0.193 REMARK 3 R VALUE (WORKING SET) : 0.192 REMARK 3 FREE R VALUE : 0.224 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.800 REMARK 3 FREE R VALUE TEST SET COUNT : 576 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) : 2.29 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.35 REMARK 3 REFLECTION IN BIN (WORKING SET) : 695 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 82.90 REMARK 3 BIN R VALUE (WORKING SET) : 0.2320 REMARK 3 BIN FREE R VALUE SET COUNT : 32 REMARK 3 BIN FREE R VALUE : 0.2630 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 1173 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 31 REMARK 3 SOLVENT ATOMS : 38 REMARK 3 REMARK 3 B VALUES. REMARK 3 B VALUE TYPE : LIKELY RESIDUAL REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 43.69 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 2.16000 REMARK 3 B22 (A**2) : 2.16000 REMARK 3 B33 (A**2) : -4.33000 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): 0.196 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.173 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.111 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 8.047 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.958 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.938 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 1219 ; 0.013 ; 0.022 REMARK 3 BOND LENGTHS OTHERS (A): NULL ; NULL ; NULL REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 1627 ; 1.501 ; 1.961 REMARK 3 BOND ANGLES OTHERS (DEGREES): NULL ; NULL ; NULL REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 150 ; 4.854 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 61 ;33.229 ;23.443 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 212 ;16.946 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 12 ;17.577 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 168 ; 0.101 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 927 ; 0.005 ; 0.020 REMARK 3 GENERAL PLANES OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): 555 ; 0.207 ; 0.200 REMARK 3 NON-BONDED CONTACTS OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION REFINED ATOMS (A): 815 ; 0.304 ; 0.200 REMARK 3 NON-BONDED TORSION OTHERS (A): NULL ; NULL ; NULL REMARK 3 H-BOND (X...Y) REFINED ATOMS (A): 62 ; 0.145 ; 0.200 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): 34 ; 0.205 ; 0.200 REMARK 3 SYMMETRY VDW OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY H-BOND REFINED ATOMS (A): 8 ; 0.173 ; 0.200 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): 761 ; 0.797 ; 1.500 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 1177 ; 1.277 ; 2.000 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 523 ; 2.282 ; 3.000 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 448 ; 3.570 ; 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 : NULL REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : 3 REMARK 3 REMARK 3 TLS GROUP : 1 REMARK 3 NUMBER OF COMPONENTS GROUP : 1 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : A 456 A 472 REMARK 3 ORIGIN FOR THE GROUP (A): 34.0369 -7.2752 11.6380 REMARK 3 T TENSOR REMARK 3 T11: 0.2326 T22: 0.3778 REMARK 3 T33: 0.0742 T12: 0.1587 REMARK 3 T13: 0.2666 T23: -0.0053 REMARK 3 L TENSOR REMARK 3 L11: 14.2058 L22: 15.1387 REMARK 3 L33: 5.0194 L12: -3.4410 REMARK 3 L13: -1.0867 L23: -8.1400 REMARK 3 S TENSOR REMARK 3 S11: 0.7017 S12: 0.1273 S13: -1.8014 REMARK 3 S21: -0.6157 S22: -1.0545 S23: -0.9225 REMARK 3 S31: 1.3654 S32: 0.5934 S33: 0.3528 REMARK 3 REMARK 3 TLS GROUP : 2 REMARK 3 NUMBER OF COMPONENTS GROUP : 1 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : A 473 A 543 REMARK 3 ORIGIN FOR THE GROUP (A): 21.0966 0.9313 13.6057 REMARK 3 T TENSOR REMARK 3 T11: 0.0650 T22: 0.1246 REMARK 3 T33: 0.0677 T12: 0.0302 REMARK 3 T13: 0.0089 T23: 0.0220 REMARK 3 L TENSOR REMARK 3 L11: 1.9657 L22: 5.4161 REMARK 3 L33: 7.3528 L12: -1.7626 REMARK 3 L13: 2.5345 L23: -4.7795 REMARK 3 S TENSOR REMARK 3 S11: -0.0322 S12: -0.2025 S13: -0.1149 REMARK 3 S21: -0.1092 S22: 0.0666 S23: 0.0596 REMARK 3 S31: 0.2174 S32: -0.3244 S33: -0.0344 REMARK 3 REMARK 3 TLS GROUP : 3 REMARK 3 NUMBER OF COMPONENTS GROUP : 1 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : A 544 A 610 REMARK 3 ORIGIN FOR THE GROUP (A): 31.3545 5.3412 17.7805 REMARK 3 T TENSOR REMARK 3 T11: 0.1528 T22: 0.2145 REMARK 3 T33: 0.1827 T12: 0.0030 REMARK 3 T13: -0.1075 T23: 0.0970 REMARK 3 L TENSOR REMARK 3 L11: 4.2940 L22: 7.3807 REMARK 3 L33: 10.8445 L12: -0.4647 REMARK 3 L13: -1.5597 L23: -2.5319 REMARK 3 S TENSOR REMARK 3 S11: -0.2171 S12: -0.2279 S13: 0.3439 REMARK 3 S21: 0.2288 S22: -0.1787 S23: -0.8617 REMARK 3 S31: -0.6085 S32: 1.0876 S33: 0.3957 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : BABINET MODEL WITH MASK REMARK 3 PARAMETERS FOR MASK CALCULATION REMARK 3 VDW PROBE RADIUS : 1.20 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 3A1B COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 01-APR-09. REMARK 100 THE DEPOSITION ID IS D_1000028686. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 10-JUN-08 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 : PHOTON FACTORY REMARK 200 BEAMLINE : BL-5A REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.0 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : MIRRORS 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 : 12159 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.292 REMARK 200 RESOLUTION RANGE LOW (A) : 32.721 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 1.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 98.3 REMARK 200 DATA REDUNDANCY : 24.10 REMARK 200 R MERGE (I) : 0.08200 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 15.0000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.29 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.38 REMARK 200 COMPLETENESS FOR SHELL (%) : 86.9 REMARK 200 DATA REDUNDANCY IN SHELL : 15.50 REMARK 200 R MERGE FOR SHELL (I) : 0.42800 REMARK 200 R SYM FOR SHELL (I) : NULL 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: MOLREP REMARK 200 STARTING MODEL: PDB ENTRY 3A1A REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 65.58 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 3.57 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 10% PEG 2000 MONOMETHYL ETHER, 0.1M REMARK 280 BIS-TRIS, PH 5.5, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 293K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 41 21 2 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,-Y,Z+1/2 REMARK 290 3555 -Y+1/2,X+1/2,Z+1/4 REMARK 290 4555 Y+1/2,-X+1/2,Z+3/4 REMARK 290 5555 -X+1/2,Y+1/2,-Z+1/4 REMARK 290 6555 X+1/2,-Y+1/2,-Z+3/4 REMARK 290 7555 Y,X,-Z REMARK 290 8555 -Y,-X,-Z+1/2 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 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 54.97500 REMARK 290 SMTRY1 3 0.000000 -1.000000 0.000000 34.27350 REMARK 290 SMTRY2 3 1.000000 0.000000 0.000000 34.27350 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 27.48750 REMARK 290 SMTRY1 4 0.000000 1.000000 0.000000 34.27350 REMARK 290 SMTRY2 4 -1.000000 0.000000 0.000000 34.27350 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 82.46250 REMARK 290 SMTRY1 5 -1.000000 0.000000 0.000000 34.27350 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 34.27350 REMARK 290 SMTRY3 5 0.000000 0.000000 -1.000000 27.48750 REMARK 290 SMTRY1 6 1.000000 0.000000 0.000000 34.27350 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 34.27350 REMARK 290 SMTRY3 6 0.000000 0.000000 -1.000000 82.46250 REMARK 290 SMTRY1 7 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY2 7 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 8 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY2 8 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 8 0.000000 0.000000 -1.000000 54.97500 REMARK 290 REMARK 290 REMARK: NULL REMARK 300 REMARK 300 BIOMOLECULE: 1 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 SOFTWARE DETERMINED QUATERNARY STRUCTURE: MONOMERIC REMARK 350 SOFTWARE USED: PISA 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 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 SER A 465 REMARK 465 THR A 466 REMARK 465 GLY A 467 REMARK 465 GLY A 468 REMARK 465 LYS A 469 REMARK 465 ALA A 470 REMARK 465 PRO A 471 REMARK 465 ASN A 611 REMARK 465 ASN A 612 REMARK 465 HIS A 613 REMARK 465 ASP A 614 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 ARG A 463 CG CD NE CZ NH1 NH2 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 ARG A 463 CB ARG A 463 CG -0.223 REMARK 500 REMARK 500 REMARK: NULL 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 LEU A 504 CA - CB - CG ANGL. DEV. = 15.4 DEGREES 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 1 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS A 494 SG REMARK 620 2 CYS A 497 SG 113.8 REMARK 620 3 CYS A 514 SG 113.1 112.2 REMARK 620 4 CYS A 517 SG 107.3 106.7 102.8 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 ZN A 2 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS A 537 SG REMARK 620 2 CYS A 540 SG 106.8 REMARK 620 3 CYS A 559 SG 111.4 109.9 REMARK 620 4 CYS A 562 SG 114.1 108.6 105.9 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 ZN A 3 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS A 549 SG REMARK 620 2 CYS A 554 SG 109.8 REMARK 620 3 CYS A 583 SG 112.4 107.5 REMARK 620 4 CYS A 586 SG 107.3 100.7 118.4 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 1 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ZN A 2 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ZN A 3 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE EDO A 615 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE EDO A 616 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE EDO A 617 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC7 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE EDO A 4 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC8 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE EDO A 5 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC9 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE EDO A 6 REMARK 800 REMARK 800 SITE_IDENTIFIER: BC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE EDO A 7 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 3A1A RELATED DB: PDB REMARK 900 THE SAME PROTEIN IN THE FREE STATE DBREF 3A1B A 456 475 UNP P68431 H31_HUMAN 2 21 DBREF 3A1B A 476 614 UNP Q9Y6K1 DNM3A_HUMAN 476 614 SEQRES 1 A 159 ALA ARG THR LYS GLN THR ALA ARG LYS SER THR GLY GLY SEQRES 2 A 159 LYS ALA PRO ARG LYS GLN LEU ARG GLU ARG LEU VAL TYR SEQRES 3 A 159 GLU VAL ARG GLN LYS CYS ARG ASN ILE GLU ASP ILE CYS SEQRES 4 A 159 ILE SER CYS GLY SER LEU ASN VAL THR LEU GLU HIS PRO SEQRES 5 A 159 LEU PHE VAL GLY GLY MET CYS GLN ASN CYS LYS ASN CYS SEQRES 6 A 159 PHE LEU GLU CYS ALA TYR GLN TYR ASP ASP ASP GLY TYR SEQRES 7 A 159 GLN SER TYR CYS THR ILE CYS CYS GLY GLY ARG GLU VAL SEQRES 8 A 159 LEU MET CYS GLY ASN ASN ASN CYS CYS ARG CYS PHE CYS SEQRES 9 A 159 VAL GLU CYS VAL ASP LEU LEU VAL GLY PRO GLY ALA ALA SEQRES 10 A 159 GLN ALA ALA ILE LYS GLU ASP PRO TRP ASN CYS TYR MET SEQRES 11 A 159 CYS GLY HIS LYS GLY THR TYR GLY LEU LEU ARG ARG ARG SEQRES 12 A 159 GLU ASP TRP PRO SER ARG LEU GLN MET PHE PHE ALA ASN SEQRES 13 A 159 ASN HIS ASP HET ZN A 1 1 HET ZN A 2 1 HET ZN A 3 1 HET EDO A 615 4 HET EDO A 616 4 HET EDO A 617 4 HET EDO A 4 4 HET EDO A 5 4 HET EDO A 6 4 HET EDO A 7 4 HETNAM ZN ZINC ION HETNAM EDO 1,2-ETHANEDIOL HETSYN EDO ETHYLENE GLYCOL FORMUL 2 ZN 3(ZN 2+) FORMUL 5 EDO 7(C2 H6 O2) FORMUL 12 HOH *38(H2 O) HELIX 1 1 ARG A 472 GLN A 485 1 14 HELIX 2 2 ASN A 489 ILE A 493 5 5 HELIX 3 3 CYS A 514 ALA A 525 1 12 HELIX 4 4 VAL A 560 VAL A 567 1 8 HELIX 5 5 GLY A 570 LYS A 577 1 8 HELIX 6 6 ASP A 600 ALA A 610 1 11 SHEET 1 A 3 ARG A 457 GLN A 460 0 SHEET 2 A 3 GLU A 545 MET A 548 -1 O MET A 548 N ARG A 457 SHEET 3 A 3 CYS A 557 CYS A 559 -1 O PHE A 558 N LEU A 547 SHEET 1 B 2 LEU A 504 GLU A 505 0 SHEET 2 B 2 GLY A 512 MET A 513 -1 O MET A 513 N LEU A 504 SHEET 1 C 2 THR A 591 TYR A 592 0 SHEET 2 C 2 LEU A 595 ARG A 596 -1 O LEU A 595 N TYR A 592 LINK ZN ZN A 1 SG CYS A 494 1555 1555 2.27 LINK ZN ZN A 1 SG CYS A 497 1555 1555 2.30 LINK ZN ZN A 1 SG CYS A 514 1555 1555 2.31 LINK ZN ZN A 1 SG CYS A 517 1555 1555 2.38 LINK ZN ZN A 2 SG CYS A 537 1555 1555 2.40 LINK ZN ZN A 2 SG CYS A 540 1555 1555 2.34 LINK ZN ZN A 2 SG CYS A 559 1555 1555 2.34 LINK ZN ZN A 2 SG CYS A 562 1555 1555 2.37 LINK ZN ZN A 3 SG CYS A 549 1555 1555 2.15 LINK ZN ZN A 3 SG CYS A 554 1555 1555 2.35 LINK ZN ZN A 3 SG CYS A 583 1555 1555 2.38 LINK ZN ZN A 3 SG CYS A 586 1555 1555 2.21 CISPEP 1 ASP A 579 PRO A 580 0 -2.35 SITE 1 AC1 4 CYS A 494 CYS A 497 CYS A 514 CYS A 517 SITE 1 AC2 4 CYS A 537 CYS A 540 CYS A 559 CYS A 562 SITE 1 AC3 4 CYS A 549 CYS A 554 CYS A 583 CYS A 586 SITE 1 AC4 8 EDO A 7 HOH A 9 PHE A 521 CYS A 524 SITE 2 AC4 8 GLN A 534 TYR A 536 CYS A 537 ARG A 556 SITE 1 AC5 6 GLU A 491 LEU A 504 GLU A 505 GLY A 511 SITE 2 AC5 6 GLY A 512 ARG A 598 SITE 1 AC6 6 GLU A 477 ALA A 525 TYR A 526 TYR A 528 SITE 2 AC6 6 ASP A 564 PRO A 569 SITE 1 AC7 3 TRP A 581 ASN A 582 TYR A 592 SITE 1 AC8 6 HOH A 21 ARG A 478 TYR A 481 GLU A 523 SITE 2 AC8 6 TYR A 526 GLN A 527 SITE 1 AC9 6 GLY A 543 ARG A 544 GLU A 545 CYS A 559 SITE 2 AC9 6 VAL A 560 GLU A 561 SITE 1 BC1 7 PHE A 521 ALA A 525 GLN A 534 ARG A 556 SITE 2 BC1 7 PRO A 569 LEU A 605 EDO A 615 CRYST1 68.547 68.547 109.950 90.00 90.00 90.00 P 41 21 2 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 0.014589 0.000000 0.000000 0.00000 SCALE2 0.000000 0.014589 0.000000 0.00000 SCALE3 0.000000 0.000000 0.009095 0.00000