HEADER TRANSFERASE 21-SEP-10 3OXF TITLE HUMAN LYSINE METHYLTRANSFERASE SMYD3 IN COMPLEX WITH ADOHCY (FORM I) COMPND MOL_ID: 1; COMPND 2 MOLECULE: SET AND MYND DOMAIN-CONTAINING PROTEIN 3; COMPND 3 CHAIN: A, B; COMPND 4 SYNONYM: ZINC FINGER MYND DOMAIN-CONTAINING PROTEIN 1; COMPND 5 EC: 2.1.1.43; COMPND 6 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 3 ORGANISM_COMMON: HUMAN; SOURCE 4 ORGANISM_TAXID: 9606; SOURCE 5 GENE: SMYD3, ZMYND1, ZNFN3A1; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 8 EXPRESSION_SYSTEM_STRAIN: BL21(DE3) CODON PLUS; SOURCE 9 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 10 EXPRESSION_SYSTEM_PLASMID: PET28B KEYWDS SMYD PROTEINS, MYND, SET DOMAIN, HISTONE LYSINE METHYLTRANSFERASE, KEYWDS 2 HISTONE METHYLATION, H3K4, TRANSFERASE EXPDTA X-RAY DIFFRACTION AUTHOR S.XU,J.WU,B.SUN,C.ZHONG,J.DING REVDAT 4 01-NOV-23 3OXF 1 REMARK SEQADV LINK REVDAT 3 08-NOV-17 3OXF 1 REMARK REVDAT 2 13-JUL-11 3OXF 1 JRNL REVDAT 1 23-FEB-11 3OXF 0 JRNL AUTH S.XU,J.WU,B.SUN,C.ZHONG,J.DING JRNL TITL STRUCTURAL AND BIOCHEMICAL STUDIES OF HUMAN LYSINE JRNL TITL 2 METHYLTRANSFERASE SMYD3 REVEAL THE IMPORTANT FUNCTIONAL JRNL TITL 3 ROLES OF ITS POST-SET AND TPR DOMAINS AND THE REGULATION OF JRNL TITL 4 ITS ACTIVITY BY DNA BINDING. JRNL REF NUCLEIC ACIDS RES. V. 39 4438 2011 JRNL REFN ISSN 0305-1048 JRNL PMID 21266482 JRNL DOI 10.1093/NAR/GKR019 REMARK 2 REMARK 2 RESOLUTION. 2.82 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.5.0109 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) : 2.82 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 50.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 97.0 REMARK 3 NUMBER OF REFLECTIONS : 26293 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) : 0.213 REMARK 3 R VALUE (WORKING SET) : 0.211 REMARK 3 FREE R VALUE : 0.261 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.000 REMARK 3 FREE R VALUE TEST SET COUNT : 1323 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) : 2.82 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.89 REMARK 3 REFLECTION IN BIN (WORKING SET) : 1608 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 83.74 REMARK 3 BIN R VALUE (WORKING SET) : 0.2780 REMARK 3 BIN FREE R VALUE SET COUNT : 71 REMARK 3 BIN FREE R VALUE : 0.3730 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 6814 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 58 REMARK 3 SOLVENT ATOMS : 24 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 40.28 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 3.85000 REMARK 3 B22 (A**2) : -4.60000 REMARK 3 B33 (A**2) : 0.74000 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : -0.31000 REMARK 3 B23 (A**2) : 0.00000 REMARK 3 REMARK 3 ESTIMATED OVERALL COORDINATE ERROR. REMARK 3 ESU BASED ON R VALUE (A): NULL REMARK 3 ESU BASED ON FREE R VALUE (A): 0.396 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): NULL REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): NULL REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.922 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.884 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 6995 ; 0.007 ; 0.022 REMARK 3 BOND LENGTHS OTHERS (A): NULL ; NULL ; NULL REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 9420 ; 1.065 ; 1.986 REMARK 3 BOND ANGLES OTHERS (DEGREES): NULL ; NULL ; NULL REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 849 ; 4.956 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 326 ;35.303 ;23.865 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 1318 ;16.327 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 58 ;18.863 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 1033 ; 0.074 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 5216 ; 0.004 ; 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): 4259 ; 0.344 ; 1.500 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 6868 ; 0.673 ; 2.000 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 2736 ; 0.846 ; 3.000 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 2552 ; 1.534 ; 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 : 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 U VALUES REMARK 4 REMARK 4 3OXF COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 05-OCT-10. REMARK 100 THE DEPOSITION ID IS D_1000061692. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 04-FEB-10 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 6.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : SSRF REMARK 200 BEAMLINE : BL17U REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.99985 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : RAYONIX MX225HE REMARK 200 INTENSITY-INTEGRATION SOFTWARE : DENZO, HKL-2000 REMARK 200 DATA SCALING SOFTWARE : SCALEPACK, HKL-2000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 26338 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.800 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 : 3.300 REMARK 200 R MERGE (I) : 0.12200 REMARK 200 R SYM (I) : NULL REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 7.6000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.80 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.90 REMARK 200 COMPLETENESS FOR SHELL (%) : 94.4 REMARK 200 DATA REDUNDANCY IN SHELL : 3.00 REMARK 200 R MERGE FOR SHELL (I) : 0.33900 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 <I/SIGMA(I)> 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: CNS REMARK 200 STARTING MODEL: 3MEK REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 56.37 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.82 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 14.4% PEG 8000, 20% GLYCEROL, 160MM REMARK 280 CALCIUM ACETATE, AND 80MM SODIUM CACODYLATE, PH 6.5, VAPOR REMARK 280 DIFFUSION, HANGING DROP, TEMPERATURE 277K 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 58.99500 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: 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 350 REMARK 350 BIOMOLECULE: 2 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: 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 MET A 1 REMARK 465 GLU A 2 REMARK 465 LEU A 429 REMARK 465 GLU A 430 REMARK 465 HIS A 431 REMARK 465 HIS A 432 REMARK 465 HIS A 433 REMARK 465 HIS A 434 REMARK 465 HIS A 435 REMARK 465 HIS A 436 REMARK 465 MET B 1 REMARK 465 ALA B 427 REMARK 465 SER B 428 REMARK 465 LEU B 429 REMARK 465 GLU B 430 REMARK 465 HIS B 431 REMARK 465 HIS B 432 REMARK 465 HIS B 433 REMARK 465 HIS B 434 REMARK 465 HIS B 435 REMARK 465 HIS B 436 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 GLU B 318 CD 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 13 9.27 -154.56 REMARK 500 ARG A 14 51.95 -117.22 REMARK 500 GLU A 57 -71.08 -52.59 REMARK 500 LYS A 84 -65.52 -27.21 REMARK 500 PRO A 167 -167.15 -65.09 REMARK 500 ALA A 168 -17.65 60.43 REMARK 500 PHE A 362 61.14 -118.87 REMARK 500 ASN B 13 42.96 -158.11 REMARK 500 ARG B 14 49.21 -153.07 REMARK 500 ARG B 51 -69.93 -91.73 REMARK 500 ASN B 134 25.76 -75.76 REMARK 500 ALA B 168 -22.46 74.76 REMARK 500 LYS B 271 -6.94 89.18 REMARK 500 MET B 385 56.51 -97.81 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 438 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS A 49 SG REMARK 620 2 CYS A 52 SG 111.0 REMARK 620 3 CYS A 71 SG 118.4 110.8 REMARK 620 4 CYS A 75 SG 109.4 107.8 98.3 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 ZN A 439 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS A 62 SG REMARK 620 2 CYS A 65 SG 123.8 REMARK 620 3 HIS A 83 NE2 111.1 106.9 REMARK 620 4 CYS A 87 SG 118.8 97.9 93.6 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 ZN A 440 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS A 208 SG REMARK 620 2 CYS A 261 SG 123.1 REMARK 620 3 CYS A 263 SG 107.9 107.7 REMARK 620 4 CYS A 266 SG 107.6 98.2 111.9 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 ZN B 438 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS B 49 SG REMARK 620 2 CYS B 52 SG 109.1 REMARK 620 3 CYS B 71 SG 105.8 108.2 REMARK 620 4 CYS B 75 SG 112.9 116.0 104.2 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 ZN B 439 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS B 62 SG REMARK 620 2 CYS B 65 SG 105.8 REMARK 620 3 HIS B 83 NE2 107.2 107.9 REMARK 620 4 CYS B 87 SG 112.9 113.5 109.3 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 ZN B 440 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS B 208 SG REMARK 620 2 CYS B 261 SG 114.1 REMARK 620 3 CYS B 263 SG 102.5 103.2 REMARK 620 4 CYS B 266 SG 101.8 103.8 131.7 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 SAH A 437 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ZN A 438 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ZN A 439 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ZN A 440 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SAH B 437 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ZN B 438 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC7 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ZN B 439 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC8 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ZN B 440 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 3OXG RELATED DB: PDB REMARK 999 REMARK 999 SEQUENCE REMARK 999 THE EXPERIMENTAL INFO OF UNIPROT (Q9H7B4, SMYD3_HUMAN) SHOWS REMARK 999 CONFLICTS K -> N, K -> R AT THE POSITIONS 13, 140 (IN REF.6: REMARK 999 AAH31010) DBREF 3OXF A 1 428 UNP Q9H7B4 SMYD3_HUMAN 1 428 DBREF 3OXF B 1 428 UNP Q9H7B4 SMYD3_HUMAN 1 428 SEQADV 3OXF ASN A 13 UNP Q9H7B4 LYS 13 SEE REMARK 999 SEQADV 3OXF ARG A 140 UNP Q9H7B4 LYS 140 SEE REMARK 999 SEQADV 3OXF LEU A 429 UNP Q9H7B4 EXPRESSION TAG SEQADV 3OXF GLU A 430 UNP Q9H7B4 EXPRESSION TAG SEQADV 3OXF HIS A 431 UNP Q9H7B4 EXPRESSION TAG SEQADV 3OXF HIS A 432 UNP Q9H7B4 EXPRESSION TAG SEQADV 3OXF HIS A 433 UNP Q9H7B4 EXPRESSION TAG SEQADV 3OXF HIS A 434 UNP Q9H7B4 EXPRESSION TAG SEQADV 3OXF HIS A 435 UNP Q9H7B4 EXPRESSION TAG SEQADV 3OXF HIS A 436 UNP Q9H7B4 EXPRESSION TAG SEQADV 3OXF ASN B 13 UNP Q9H7B4 LYS 13 SEE REMARK 999 SEQADV 3OXF ARG B 140 UNP Q9H7B4 LYS 140 SEE REMARK 999 SEQADV 3OXF LEU B 429 UNP Q9H7B4 EXPRESSION TAG SEQADV 3OXF GLU B 430 UNP Q9H7B4 EXPRESSION TAG SEQADV 3OXF HIS B 431 UNP Q9H7B4 EXPRESSION TAG SEQADV 3OXF HIS B 432 UNP Q9H7B4 EXPRESSION TAG SEQADV 3OXF HIS B 433 UNP Q9H7B4 EXPRESSION TAG SEQADV 3OXF HIS B 434 UNP Q9H7B4 EXPRESSION TAG SEQADV 3OXF HIS B 435 UNP Q9H7B4 EXPRESSION TAG SEQADV 3OXF HIS B 436 UNP Q9H7B4 EXPRESSION TAG SEQRES 1 A 436 MET GLU PRO LEU LYS VAL GLU LYS PHE ALA THR ALA ASN SEQRES 2 A 436 ARG GLY ASN GLY LEU ARG ALA VAL THR PRO LEU ARG PRO SEQRES 3 A 436 GLY GLU LEU LEU PHE ARG SER ASP PRO LEU ALA TYR THR SEQRES 4 A 436 VAL CYS LYS GLY SER ARG GLY VAL VAL CYS ASP ARG CYS SEQRES 5 A 436 LEU LEU GLY LYS GLU LYS LEU MET ARG CYS SER GLN CYS SEQRES 6 A 436 ARG VAL ALA LYS TYR CYS SER ALA LYS CYS GLN LYS LYS SEQRES 7 A 436 ALA TRP PRO ASP HIS LYS ARG GLU CYS LYS CYS LEU LYS SEQRES 8 A 436 SER CYS LYS PRO ARG TYR PRO PRO ASP SER VAL ARG LEU SEQRES 9 A 436 LEU GLY ARG VAL VAL PHE LYS LEU MET ASP GLY ALA PRO SEQRES 10 A 436 SER GLU SER GLU LYS LEU TYR SER PHE TYR ASP LEU GLU SEQRES 11 A 436 SER ASN ILE ASN LYS LEU THR GLU ASP ARG LYS GLU GLY SEQRES 12 A 436 LEU ARG GLN LEU VAL MET THR PHE GLN HIS PHE MET ARG SEQRES 13 A 436 GLU GLU ILE GLN ASP ALA SER GLN LEU PRO PRO ALA PHE SEQRES 14 A 436 ASP LEU PHE GLU ALA PHE ALA LYS VAL ILE CYS ASN SER SEQRES 15 A 436 PHE THR ILE CYS ASN ALA GLU MET GLN GLU VAL GLY VAL SEQRES 16 A 436 GLY LEU TYR PRO SER ILE SER LEU LEU ASN HIS SER CYS SEQRES 17 A 436 ASP PRO ASN CYS SER ILE VAL PHE ASN GLY PRO HIS LEU SEQRES 18 A 436 LEU LEU ARG ALA VAL ARG ASP ILE GLU VAL GLY GLU GLU SEQRES 19 A 436 LEU THR ILE CYS TYR LEU ASP MET LEU MET THR SER GLU SEQRES 20 A 436 GLU ARG ARG LYS GLN LEU ARG ASP GLN TYR CYS PHE GLU SEQRES 21 A 436 CYS ASP CYS PHE ARG CYS GLN THR GLN ASP LYS ASP ALA SEQRES 22 A 436 ASP MET LEU THR GLY ASP GLU GLN VAL TRP LYS GLU VAL SEQRES 23 A 436 GLN GLU SER LEU LYS LYS ILE GLU GLU LEU LYS ALA HIS SEQRES 24 A 436 TRP LYS TRP GLU GLN VAL LEU ALA MET CYS GLN ALA ILE SEQRES 25 A 436 ILE SER SER ASN SER GLU ARG LEU PRO ASP ILE ASN ILE SEQRES 26 A 436 TYR GLN LEU LYS VAL LEU ASP CYS ALA MET ASP ALA CYS SEQRES 27 A 436 ILE ASN LEU GLY LEU LEU GLU GLU ALA LEU PHE TYR GLY SEQRES 28 A 436 THR ARG THR MET GLU PRO TYR ARG ILE PHE PHE PRO GLY SEQRES 29 A 436 SER HIS PRO VAL ARG GLY VAL GLN VAL MET LYS VAL GLY SEQRES 30 A 436 LYS LEU GLN LEU HIS GLN GLY MET PHE PRO GLN ALA MET SEQRES 31 A 436 LYS ASN LEU ARG LEU ALA PHE ASP ILE MET ARG VAL THR SEQRES 32 A 436 HIS GLY ARG GLU HIS SER LEU ILE GLU ASP LEU ILE LEU SEQRES 33 A 436 LEU LEU GLU GLU CYS ASP ALA ASN ILE ARG ALA SER LEU SEQRES 34 A 436 GLU HIS HIS HIS HIS HIS HIS SEQRES 1 B 436 MET GLU PRO LEU LYS VAL GLU LYS PHE ALA THR ALA ASN SEQRES 2 B 436 ARG GLY ASN GLY LEU ARG ALA VAL THR PRO LEU ARG PRO SEQRES 3 B 436 GLY GLU LEU LEU PHE ARG SER ASP PRO LEU ALA TYR THR SEQRES 4 B 436 VAL CYS LYS GLY SER ARG GLY VAL VAL CYS ASP ARG CYS SEQRES 5 B 436 LEU LEU GLY LYS GLU LYS LEU MET ARG CYS SER GLN CYS SEQRES 6 B 436 ARG VAL ALA LYS TYR CYS SER ALA LYS CYS GLN LYS LYS SEQRES 7 B 436 ALA TRP PRO ASP HIS LYS ARG GLU CYS LYS CYS LEU LYS SEQRES 8 B 436 SER CYS LYS PRO ARG TYR PRO PRO ASP SER VAL ARG LEU SEQRES 9 B 436 LEU GLY ARG VAL VAL PHE LYS LEU MET ASP GLY ALA PRO SEQRES 10 B 436 SER GLU SER GLU LYS LEU TYR SER PHE TYR ASP LEU GLU SEQRES 11 B 436 SER ASN ILE ASN LYS LEU THR GLU ASP ARG LYS GLU GLY SEQRES 12 B 436 LEU ARG GLN LEU VAL MET THR PHE GLN HIS PHE MET ARG SEQRES 13 B 436 GLU GLU ILE GLN ASP ALA SER GLN LEU PRO PRO ALA PHE SEQRES 14 B 436 ASP LEU PHE GLU ALA PHE ALA LYS VAL ILE CYS ASN SER SEQRES 15 B 436 PHE THR ILE CYS ASN ALA GLU MET GLN GLU VAL GLY VAL SEQRES 16 B 436 GLY LEU TYR PRO SER ILE SER LEU LEU ASN HIS SER CYS SEQRES 17 B 436 ASP PRO ASN CYS SER ILE VAL PHE ASN GLY PRO HIS LEU SEQRES 18 B 436 LEU LEU ARG ALA VAL ARG ASP ILE GLU VAL GLY GLU GLU SEQRES 19 B 436 LEU THR ILE CYS TYR LEU ASP MET LEU MET THR SER GLU SEQRES 20 B 436 GLU ARG ARG LYS GLN LEU ARG ASP GLN TYR CYS PHE GLU SEQRES 21 B 436 CYS ASP CYS PHE ARG CYS GLN THR GLN ASP LYS ASP ALA SEQRES 22 B 436 ASP MET LEU THR GLY ASP GLU GLN VAL TRP LYS GLU VAL SEQRES 23 B 436 GLN GLU SER LEU LYS LYS ILE GLU GLU LEU LYS ALA HIS SEQRES 24 B 436 TRP LYS TRP GLU GLN VAL LEU ALA MET CYS GLN ALA ILE SEQRES 25 B 436 ILE SER SER ASN SER GLU ARG LEU PRO ASP ILE ASN ILE SEQRES 26 B 436 TYR GLN LEU LYS VAL LEU ASP CYS ALA MET ASP ALA CYS SEQRES 27 B 436 ILE ASN LEU GLY LEU LEU GLU GLU ALA LEU PHE TYR GLY SEQRES 28 B 436 THR ARG THR MET GLU PRO TYR ARG ILE PHE PHE PRO GLY SEQRES 29 B 436 SER HIS PRO VAL ARG GLY VAL GLN VAL MET LYS VAL GLY SEQRES 30 B 436 LYS LEU GLN LEU HIS GLN GLY MET PHE PRO GLN ALA MET SEQRES 31 B 436 LYS ASN LEU ARG LEU ALA PHE ASP ILE MET ARG VAL THR SEQRES 32 B 436 HIS GLY ARG GLU HIS SER LEU ILE GLU ASP LEU ILE LEU SEQRES 33 B 436 LEU LEU GLU GLU CYS ASP ALA ASN ILE ARG ALA SER LEU SEQRES 34 B 436 GLU HIS HIS HIS HIS HIS HIS HET SAH A 437 26 HET ZN A 438 1 HET ZN A 439 1 HET ZN A 440 1 HET SAH B 437 26 HET ZN B 438 1 HET ZN B 439 1 HET ZN B 440 1 HETNAM SAH S-ADENOSYL-L-HOMOCYSTEINE HETNAM ZN ZINC ION FORMUL 3 SAH 2(C14 H20 N6 O5 S) FORMUL 4 ZN 6(ZN 2+) FORMUL 11 HOH *24(H2 O) HELIX 1 1 LYS A 42 ARG A 45 5 4 HELIX 2 2 SER A 72 LYS A 84 1 13 HELIX 3 3 GLU A 86 LYS A 94 1 9 HELIX 4 4 PRO A 99 LEU A 112 1 14 HELIX 5 5 SER A 118 LYS A 122 5 5 HELIX 6 6 ASN A 132 LEU A 136 5 5 HELIX 7 7 THR A 137 MET A 155 1 19 HELIX 8 8 ASP A 161 LEU A 165 5 5 HELIX 9 9 ASP A 170 SER A 182 1 13 HELIX 10 10 SER A 200 LEU A 204 5 5 HELIX 11 11 THR A 245 CYS A 258 1 14 HELIX 12 12 CYS A 263 THR A 268 1 6 HELIX 13 13 LYS A 271 LEU A 276 1 6 HELIX 14 14 ASP A 279 HIS A 299 1 21 HELIX 15 15 LYS A 301 SER A 317 1 17 HELIX 16 16 ASN A 324 GLY A 342 1 19 HELIX 17 17 LEU A 343 ARG A 353 1 11 HELIX 18 18 THR A 354 PHE A 362 1 9 HELIX 19 19 HIS A 366 GLN A 383 1 18 HELIX 20 20 MET A 385 HIS A 404 1 20 HELIX 21 21 SER A 409 SER A 428 1 20 HELIX 22 22 SER B 72 ALA B 79 1 8 HELIX 23 23 ALA B 79 LYS B 84 1 6 HELIX 24 24 GLU B 86 SER B 92 1 7 HELIX 25 25 PRO B 99 LEU B 112 1 14 HELIX 26 26 SER B 118 LYS B 122 5 5 HELIX 27 27 ASN B 132 LEU B 136 5 5 HELIX 28 28 THR B 137 MET B 155 1 19 HELIX 29 29 ASP B 161 LEU B 165 5 5 HELIX 30 30 ASP B 170 SER B 182 1 13 HELIX 31 31 SER B 200 LEU B 204 5 5 HELIX 32 32 THR B 245 GLN B 256 1 12 HELIX 33 33 CYS B 263 GLN B 269 1 7 HELIX 34 34 LYS B 271 LEU B 276 1 6 HELIX 35 35 ASP B 279 HIS B 299 1 21 HELIX 36 36 LYS B 301 SER B 317 1 17 HELIX 37 37 ASN B 324 GLY B 342 1 19 HELIX 38 38 LEU B 343 PHE B 362 1 20 HELIX 39 39 HIS B 366 GLN B 383 1 18 HELIX 40 40 MET B 385 HIS B 404 1 20 HELIX 41 41 HIS B 408 ASN B 424 1 17 SHEET 1 A 2 VAL A 6 ALA A 10 0 SHEET 2 A 2 ASN A 16 ALA A 20 -1 O GLY A 17 N PHE A 9 SHEET 1 B 3 LEU A 29 SER A 33 0 SHEET 2 B 3 HIS A 220 ALA A 225 -1 O LEU A 223 N LEU A 30 SHEET 3 B 3 CYS A 212 ASN A 217 -1 N ASN A 217 O HIS A 220 SHEET 1 C 3 ALA A 37 VAL A 40 0 SHEET 2 C 3 GLU A 192 LEU A 197 -1 O LEU A 197 N ALA A 37 SHEET 3 C 3 PHE A 183 CYS A 186 -1 N PHE A 183 O GLY A 196 SHEET 1 D 2 MET A 60 ARG A 61 0 SHEET 2 D 2 LYS A 69 TYR A 70 -1 O TYR A 70 N MET A 60 SHEET 1 E 2 ASN A 205 HIS A 206 0 SHEET 2 E 2 THR A 236 ILE A 237 1 O ILE A 237 N ASN A 205 SHEET 1 F 4 VAL B 6 ALA B 10 0 SHEET 2 F 4 ASN B 16 ALA B 20 -1 O ARG B 19 N GLU B 7 SHEET 3 F 4 GLU B 234 ILE B 237 -1 O LEU B 235 N LEU B 18 SHEET 4 F 4 ASN B 205 HIS B 206 1 N ASN B 205 O ILE B 237 SHEET 1 G 3 LEU B 29 SER B 33 0 SHEET 2 G 3 HIS B 220 ALA B 225 -1 O LEU B 221 N SER B 33 SHEET 3 G 3 CYS B 212 ASN B 217 -1 N ASN B 217 O HIS B 220 SHEET 1 H 3 ALA B 37 VAL B 40 0 SHEET 2 H 3 GLU B 192 LEU B 197 -1 O VAL B 195 N THR B 39 SHEET 3 H 3 PHE B 183 CYS B 186 -1 N PHE B 183 O GLY B 196 SHEET 1 I 2 MET B 60 ARG B 61 0 SHEET 2 I 2 LYS B 69 TYR B 70 -1 O TYR B 70 N MET B 60 LINK SG CYS A 49 ZN ZN A 438 1555 1555 2.32 LINK SG CYS A 52 ZN ZN A 438 1555 1555 2.23 LINK SG CYS A 62 ZN ZN A 439 1555 1555 2.25 LINK SG CYS A 65 ZN ZN A 439 1555 1555 2.28 LINK SG CYS A 71 ZN ZN A 438 1555 1555 2.20 LINK SG CYS A 75 ZN ZN A 438 1555 1555 2.32 LINK NE2 HIS A 83 ZN ZN A 439 1555 1555 2.08 LINK SG CYS A 87 ZN ZN A 439 1555 1555 2.21 LINK SG CYS A 208 ZN ZN A 440 1555 1555 2.22 LINK SG CYS A 261 ZN ZN A 440 1555 1555 2.21 LINK SG CYS A 263 ZN ZN A 440 1555 1555 2.22 LINK SG CYS A 266 ZN ZN A 440 1555 1555 2.21 LINK SG CYS B 49 ZN ZN B 438 1555 1555 2.43 LINK SG CYS B 52 ZN ZN B 438 1555 1555 2.37 LINK SG CYS B 62 ZN ZN B 439 1555 1555 2.21 LINK SG CYS B 65 ZN ZN B 439 1555 1555 2.32 LINK SG CYS B 71 ZN ZN B 438 1555 1555 2.28 LINK SG CYS B 75 ZN ZN B 438 1555 1555 2.22 LINK NE2 HIS B 83 ZN ZN B 439 1555 1555 2.12 LINK SG CYS B 87 ZN ZN B 439 1555 1555 2.21 LINK SG CYS B 208 ZN ZN B 440 1555 1555 2.46 LINK SG CYS B 261 ZN ZN B 440 1555 1555 2.34 LINK SG CYS B 263 ZN ZN B 440 1555 1555 2.37 LINK SG CYS B 266 ZN ZN B 440 1555 1555 2.24 CISPEP 1 LYS A 94 PRO A 95 0 -1.09 CISPEP 2 LYS B 94 PRO B 95 0 9.10 SITE 1 AC1 14 ARG A 14 GLY A 15 ASN A 16 TYR A 124 SITE 2 AC1 14 GLU A 130 ASN A 132 ASN A 181 SER A 202 SITE 3 AC1 14 ASN A 205 HIS A 206 TYR A 239 TYR A 257 SITE 4 AC1 14 PHE A 259 HOH A 450 SITE 1 AC2 4 CYS A 49 CYS A 52 CYS A 71 CYS A 75 SITE 1 AC3 4 CYS A 62 CYS A 65 HIS A 83 CYS A 87 SITE 1 AC4 4 CYS A 208 CYS A 261 CYS A 263 CYS A 266 SITE 1 AC5 12 ARG B 14 GLY B 15 ASN B 16 TYR B 124 SITE 2 AC5 12 ASN B 132 SER B 202 LEU B 204 ASN B 205 SITE 3 AC5 12 HIS B 206 TYR B 239 TYR B 257 PHE B 259 SITE 1 AC6 4 CYS B 49 CYS B 52 CYS B 71 CYS B 75 SITE 1 AC7 4 CYS B 62 CYS B 65 HIS B 83 CYS B 87 SITE 1 AC8 4 CYS B 208 CYS B 261 CYS B 263 CYS B 266 CRYST1 57.991 117.990 82.808 90.00 91.78 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 0.017244 0.000000 0.000536 0.00000 SCALE2 0.000000 0.008475 0.000000 0.00000 SCALE3 0.000000 0.000000 0.012082 0.00000