PDB Short entry for 3OXG HEADER TRANSFERASE 21-SEP-10 3OXG TITLE HUMAN LYSINE METHYLTRANSFERASE SMYD3 IN COMPLEX WITH ADOHCY (FORM III) COMPND MOL_ID: 1; COMPND 2 MOLECULE: SET AND MYND DOMAIN-CONTAINING PROTEIN 3; COMPND 3 CHAIN: A; 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: PET28A 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 3 01-NOV-23 3OXG 1 REMARK SEQADV LINK REVDAT 2 13-JUL-11 3OXG 1 JRNL REVDAT 1 23-FEB-11 3OXG 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. 3.41 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) : 3.41 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 50.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.7 REMARK 3 NUMBER OF REFLECTIONS : 9353 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) : 0.225 REMARK 3 R VALUE (WORKING SET) : 0.224 REMARK 3 FREE R VALUE : 0.249 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.200 REMARK 3 FREE R VALUE TEST SET COUNT : 487 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) : 3.41 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 3.49 REMARK 3 REFLECTION IN BIN (WORKING SET) : 624 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 98.36 REMARK 3 BIN R VALUE (WORKING SET) : 0.3310 REMARK 3 BIN FREE R VALUE SET COUNT : 37 REMARK 3 BIN FREE R VALUE : 0.3730 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 3397 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 29 REMARK 3 SOLVENT ATOMS : 0 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 97.44 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -1.08000 REMARK 3 B22 (A**2) : -1.08000 REMARK 3 B33 (A**2) : 1.62000 REMARK 3 B12 (A**2) : -0.54000 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): NULL REMARK 3 ESU BASED ON FREE R VALUE (A): 0.538 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.430 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 28.340 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.928 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.916 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 3489 ; 0.008 ; 0.022 REMARK 3 BOND LENGTHS OTHERS (A): NULL ; NULL ; NULL REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 4698 ; 1.095 ; 1.986 REMARK 3 BOND ANGLES OTHERS (DEGREES): NULL ; NULL ; NULL REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 423 ; 4.919 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 163 ;37.669 ;23.865 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 658 ;17.200 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 29 ;17.355 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 515 ; 0.071 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 2600 ; 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): 2122 ; 0.478 ; 1.500 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 3422 ; 0.830 ; 2.000 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 1367 ; 0.631 ; 3.000 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 1276 ; 1.143 ; 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: U VALUES: REFINED INDIVIDUALLY REMARK 4 REMARK 4 3OXG 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_1000061693. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 23-JUN-10 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 9.0 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) : 0.97908 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 : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : HKL-2000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 9395 REMARK 200 RESOLUTION RANGE HIGH (A) : 3.400 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 (%) : 99.9 REMARK 200 DATA REDUNDANCY : 7.400 REMARK 200 R MERGE (I) : 0.13000 REMARK 200 R SYM (I) : NULL REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : NULL REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 3.40 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 3.52 REMARK 200 COMPLETENESS FOR SHELL (%) : 100.0 REMARK 200 DATA REDUNDANCY IN SHELL : 5.90 REMARK 200 R MERGE FOR SHELL (I) : 0.64900 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 <I/SIGMA(I)> FOR SHELL : 2.500 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: 3OXF REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 62.37 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 3.27 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 20% POLYETHYLENE GLYCOL MONOMETHYL REMARK 280 ETHER 550, 0.1M NACL, 0.1M BICINE, PH 9.0, VAPOR DIFFUSION, REMARK 280 SITTING DROP, TEMPERATURE 277K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 61 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -Y,X-Y,Z+1/3 REMARK 290 3555 -X+Y,-X,Z+2/3 REMARK 290 4555 -X,-Y,Z+1/2 REMARK 290 5555 Y,-X+Y,Z+5/6 REMARK 290 6555 X-Y,X,Z+1/6 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 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 2 0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 37.40067 REMARK 290 SMTRY1 3 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 3 -0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 74.80133 REMARK 290 SMTRY1 4 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 56.10100 REMARK 290 SMTRY1 5 0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 5 -0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 5 0.000000 0.000000 1.000000 93.50167 REMARK 290 SMTRY1 6 0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 6 0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 6 0.000000 0.000000 1.000000 18.70033 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 MET A -35 REMARK 465 GLY A -34 REMARK 465 SER A -33 REMARK 465 SER A -32 REMARK 465 HIS A -31 REMARK 465 HIS A -30 REMARK 465 HIS A -29 REMARK 465 HIS A -28 REMARK 465 HIS A -27 REMARK 465 HIS A -26 REMARK 465 SER A -25 REMARK 465 SER A -24 REMARK 465 GLY A -23 REMARK 465 LEU A -22 REMARK 465 VAL A -21 REMARK 465 PRO A -20 REMARK 465 ARG A -19 REMARK 465 GLY A -18 REMARK 465 SER A -17 REMARK 465 HIS A -16 REMARK 465 MET A -15 REMARK 465 ALA A -14 REMARK 465 SER A -13 REMARK 465 MET A -12 REMARK 465 THR A -11 REMARK 465 GLY A -10 REMARK 465 GLY A -9 REMARK 465 GLN A -8 REMARK 465 GLN A -7 REMARK 465 MET A -6 REMARK 465 GLY A -5 REMARK 465 ARG A -4 REMARK 465 GLY A -3 REMARK 465 SER A -2 REMARK 465 GLU A -1 REMARK 465 PHE A 0 REMARK 465 MET A 1 REMARK 465 GLU A 2 REMARK 465 ALA A 427 REMARK 465 SER A 428 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 -5.44 -143.38 REMARK 500 ARG A 14 74.64 -114.11 REMARK 500 ASN A 16 -164.31 -113.41 REMARK 500 ASP A 50 7.22 -56.83 REMARK 500 ARG A 51 -84.82 -132.92 REMARK 500 GLU A 57 167.34 -45.92 REMARK 500 LYS A 58 93.06 14.61 REMARK 500 CYS A 62 121.05 -31.51 REMARK 500 GLN A 64 -75.64 -72.55 REMARK 500 VAL A 67 -54.84 -132.29 REMARK 500 LYS A 94 122.23 -27.77 REMARK 500 PRO A 117 65.43 -66.32 REMARK 500 THR A 137 -158.21 -74.86 REMARK 500 GLU A 189 20.56 -75.21 REMARK 500 LEU A 243 56.15 -94.82 REMARK 500 SER A 246 -36.04 -39.14 REMARK 500 CYS A 258 51.92 71.39 REMARK 500 PHE A 264 -60.79 -24.89 REMARK 500 GLN A 269 60.69 36.99 REMARK 500 LYS A 271 4.79 58.98 REMARK 500 TRP A 302 -82.68 15.77 REMARK 500 GLU A 303 -51.03 -27.96 REMARK 500 ARG A 319 -60.36 -121.53 REMARK 500 MET A 385 47.48 -96.79 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 429 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS A 49 SG REMARK 620 2 CYS A 52 SG 110.3 REMARK 620 3 CYS A 71 SG 128.3 104.3 REMARK 620 4 CYS A 75 SG 106.2 117.2 90.0 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 ZN A 430 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS A 62 SG REMARK 620 2 CYS A 65 SG 106.9 REMARK 620 3 HIS A 83 NE2 99.3 111.8 REMARK 620 4 CYS A 87 SG 108.1 126.5 100.9 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 ZN A 431 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS A 208 SG REMARK 620 2 CYS A 261 SG 113.2 REMARK 620 3 CYS A 263 SG 87.7 132.3 REMARK 620 4 CYS A 266 SG 92.1 108.5 113.2 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 429 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ZN A 430 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ZN A 431 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SAH A 432 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 3OXF 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 3OXG A 1 428 UNP Q9H7B4 SMYD3_HUMAN 1 428 SEQADV 3OXG MET A -35 UNP Q9H7B4 EXPRESSION TAG SEQADV 3OXG GLY A -34 UNP Q9H7B4 EXPRESSION TAG SEQADV 3OXG SER A -33 UNP Q9H7B4 EXPRESSION TAG SEQADV 3OXG SER A -32 UNP Q9H7B4 EXPRESSION TAG SEQADV 3OXG HIS A -31 UNP Q9H7B4 EXPRESSION TAG SEQADV 3OXG HIS A -30 UNP Q9H7B4 EXPRESSION TAG SEQADV 3OXG HIS A -29 UNP Q9H7B4 EXPRESSION TAG SEQADV 3OXG HIS A -28 UNP Q9H7B4 EXPRESSION TAG SEQADV 3OXG HIS A -27 UNP Q9H7B4 EXPRESSION TAG SEQADV 3OXG HIS A -26 UNP Q9H7B4 EXPRESSION TAG SEQADV 3OXG SER A -25 UNP Q9H7B4 EXPRESSION TAG SEQADV 3OXG SER A -24 UNP Q9H7B4 EXPRESSION TAG SEQADV 3OXG GLY A -23 UNP Q9H7B4 EXPRESSION TAG SEQADV 3OXG LEU A -22 UNP Q9H7B4 EXPRESSION TAG SEQADV 3OXG VAL A -21 UNP Q9H7B4 EXPRESSION TAG SEQADV 3OXG PRO A -20 UNP Q9H7B4 EXPRESSION TAG SEQADV 3OXG ARG A -19 UNP Q9H7B4 EXPRESSION TAG SEQADV 3OXG GLY A -18 UNP Q9H7B4 EXPRESSION TAG SEQADV 3OXG SER A -17 UNP Q9H7B4 EXPRESSION TAG SEQADV 3OXG HIS A -16 UNP Q9H7B4 EXPRESSION TAG SEQADV 3OXG MET A -15 UNP Q9H7B4 EXPRESSION TAG SEQADV 3OXG ALA A -14 UNP Q9H7B4 EXPRESSION TAG SEQADV 3OXG SER A -13 UNP Q9H7B4 EXPRESSION TAG SEQADV 3OXG MET A -12 UNP Q9H7B4 EXPRESSION TAG SEQADV 3OXG THR A -11 UNP Q9H7B4 EXPRESSION TAG SEQADV 3OXG GLY A -10 UNP Q9H7B4 EXPRESSION TAG SEQADV 3OXG GLY A -9 UNP Q9H7B4 EXPRESSION TAG SEQADV 3OXG GLN A -8 UNP Q9H7B4 EXPRESSION TAG SEQADV 3OXG GLN A -7 UNP Q9H7B4 EXPRESSION TAG SEQADV 3OXG MET A -6 UNP Q9H7B4 EXPRESSION TAG SEQADV 3OXG GLY A -5 UNP Q9H7B4 EXPRESSION TAG SEQADV 3OXG ARG A -4 UNP Q9H7B4 EXPRESSION TAG SEQADV 3OXG GLY A -3 UNP Q9H7B4 EXPRESSION TAG SEQADV 3OXG SER A -2 UNP Q9H7B4 EXPRESSION TAG SEQADV 3OXG GLU A -1 UNP Q9H7B4 EXPRESSION TAG SEQADV 3OXG PHE A 0 UNP Q9H7B4 EXPRESSION TAG SEQADV 3OXG ASN A 13 UNP Q9H7B4 LYS 13 SEE REMARK 999 SEQADV 3OXG ARG A 140 UNP Q9H7B4 LYS 140 SEE REMARK 999 SEQRES 1 A 464 MET GLY SER SER HIS HIS HIS HIS HIS HIS SER SER GLY SEQRES 2 A 464 LEU VAL PRO ARG GLY SER HIS MET ALA SER MET THR GLY SEQRES 3 A 464 GLY GLN GLN MET GLY ARG GLY SER GLU PHE MET GLU PRO SEQRES 4 A 464 LEU LYS VAL GLU LYS PHE ALA THR ALA ASN ARG GLY ASN SEQRES 5 A 464 GLY LEU ARG ALA VAL THR PRO LEU ARG PRO GLY GLU LEU SEQRES 6 A 464 LEU PHE ARG SER ASP PRO LEU ALA TYR THR VAL CYS LYS SEQRES 7 A 464 GLY SER ARG GLY VAL VAL CYS ASP ARG CYS LEU LEU GLY SEQRES 8 A 464 LYS GLU LYS LEU MET ARG CYS SER GLN CYS ARG VAL ALA SEQRES 9 A 464 LYS TYR CYS SER ALA LYS CYS GLN LYS LYS ALA TRP PRO SEQRES 10 A 464 ASP HIS LYS ARG GLU CYS LYS CYS LEU LYS SER CYS LYS SEQRES 11 A 464 PRO ARG TYR PRO PRO ASP SER VAL ARG LEU LEU GLY ARG SEQRES 12 A 464 VAL VAL PHE LYS LEU MET ASP GLY ALA PRO SER GLU SER SEQRES 13 A 464 GLU LYS LEU TYR SER PHE TYR ASP LEU GLU SER ASN ILE SEQRES 14 A 464 ASN LYS LEU THR GLU ASP ARG LYS GLU GLY LEU ARG GLN SEQRES 15 A 464 LEU VAL MET THR PHE GLN HIS PHE MET ARG GLU GLU ILE SEQRES 16 A 464 GLN ASP ALA SER GLN LEU PRO PRO ALA PHE ASP LEU PHE SEQRES 17 A 464 GLU ALA PHE ALA LYS VAL ILE CYS ASN SER PHE THR ILE SEQRES 18 A 464 CYS ASN ALA GLU MET GLN GLU VAL GLY VAL GLY LEU TYR SEQRES 19 A 464 PRO SER ILE SER LEU LEU ASN HIS SER CYS ASP PRO ASN SEQRES 20 A 464 CYS SER ILE VAL PHE ASN GLY PRO HIS LEU LEU LEU ARG SEQRES 21 A 464 ALA VAL ARG ASP ILE GLU VAL GLY GLU GLU LEU THR ILE SEQRES 22 A 464 CYS TYR LEU ASP MET LEU MET THR SER GLU GLU ARG ARG SEQRES 23 A 464 LYS GLN LEU ARG ASP GLN TYR CYS PHE GLU CYS ASP CYS SEQRES 24 A 464 PHE ARG CYS GLN THR GLN ASP LYS ASP ALA ASP MET LEU SEQRES 25 A 464 THR GLY ASP GLU GLN VAL TRP LYS GLU VAL GLN GLU SER SEQRES 26 A 464 LEU LYS LYS ILE GLU GLU LEU LYS ALA HIS TRP LYS TRP SEQRES 27 A 464 GLU GLN VAL LEU ALA MET CYS GLN ALA ILE ILE SER SER SEQRES 28 A 464 ASN SER GLU ARG LEU PRO ASP ILE ASN ILE TYR GLN LEU SEQRES 29 A 464 LYS VAL LEU ASP CYS ALA MET ASP ALA CYS ILE ASN LEU SEQRES 30 A 464 GLY LEU LEU GLU GLU ALA LEU PHE TYR GLY THR ARG THR SEQRES 31 A 464 MET GLU PRO TYR ARG ILE PHE PHE PRO GLY SER HIS PRO SEQRES 32 A 464 VAL ARG GLY VAL GLN VAL MET LYS VAL GLY LYS LEU GLN SEQRES 33 A 464 LEU HIS GLN GLY MET PHE PRO GLN ALA MET LYS ASN LEU SEQRES 34 A 464 ARG LEU ALA PHE ASP ILE MET ARG VAL THR HIS GLY ARG SEQRES 35 A 464 GLU HIS SER LEU ILE GLU ASP LEU ILE LEU LEU LEU GLU SEQRES 36 A 464 GLU CYS ASP ALA ASN ILE ARG ALA SER HET ZN A 429 1 HET ZN A 430 1 HET ZN A 431 1 HET SAH A 432 26 HETNAM ZN ZINC ION HETNAM SAH S-ADENOSYL-L-HOMOCYSTEINE FORMUL 2 ZN 3(ZN 2+) FORMUL 5 SAH C14 H20 N6 O5 S HELIX 1 1 SER A 72 LYS A 94 1 23 HELIX 2 2 PRO A 99 LEU A 112 1 14 HELIX 3 3 SER A 118 LYS A 122 5 5 HELIX 4 4 ASN A 132 LEU A 136 5 5 HELIX 5 5 THR A 137 MET A 155 1 19 HELIX 6 6 ASP A 170 ASN A 181 1 12 HELIX 7 7 SER A 200 LEU A 204 5 5 HELIX 8 8 THR A 245 TYR A 257 1 13 HELIX 9 9 CYS A 263 THR A 268 1 6 HELIX 10 10 LYS A 271 THR A 277 1 7 HELIX 11 11 ASP A 279 HIS A 299 1 21 HELIX 12 12 TRP A 302 ASN A 316 1 15 HELIX 13 13 ASN A 324 GLY A 342 1 19 HELIX 14 14 LEU A 343 THR A 352 1 10 HELIX 15 15 THR A 354 PHE A 362 1 9 HELIX 16 16 HIS A 366 GLY A 384 1 19 HELIX 17 17 MET A 385 HIS A 404 1 20 HELIX 18 18 HIS A 408 ALA A 423 1 16 SHEET 1 A 2 VAL A 6 LYS A 8 0 SHEET 2 A 2 LEU A 18 ALA A 20 -1 O ARG A 19 N GLU A 7 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 221 N SER A 33 SHEET 3 B 3 CYS A 212 ASN A 217 -1 N VAL A 215 O LEU A 222 SHEET 1 C 3 ALA A 37 VAL A 40 0 SHEET 2 C 3 GLU A 192 LEU A 197 -1 O VAL A 195 N THR A 39 SHEET 3 C 3 SER A 182 CYS A 186 -1 N ILE A 185 O GLY A 194 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 LINK SG CYS A 49 ZN ZN A 429 1555 1555 2.50 LINK SG CYS A 52 ZN ZN A 429 1555 1555 2.33 LINK SG CYS A 62 ZN ZN A 430 1555 1555 2.44 LINK SG CYS A 65 ZN ZN A 430 1555 1555 2.63 LINK SG CYS A 71 ZN ZN A 429 1555 1555 2.48 LINK SG CYS A 75 ZN ZN A 429 1555 1555 2.40 LINK NE2 HIS A 83 ZN ZN A 430 1555 1555 1.91 LINK SG CYS A 87 ZN ZN A 430 1555 1555 2.42 LINK SG CYS A 208 ZN ZN A 431 1555 1555 2.67 LINK SG CYS A 261 ZN ZN A 431 1555 1555 2.12 LINK SG CYS A 263 ZN ZN A 431 1555 1555 2.66 LINK SG CYS A 266 ZN ZN A 431 1555 1555 2.80 CISPEP 1 LYS A 94 PRO A 95 0 -3.27 SITE 1 AC1 4 CYS A 49 CYS A 52 CYS A 71 CYS A 75 SITE 1 AC2 4 CYS A 62 CYS A 65 HIS A 83 CYS A 87 SITE 1 AC3 4 CYS A 208 CYS A 261 CYS A 263 CYS A 266 SITE 1 AC4 11 ARG A 14 ASN A 16 GLY A 17 TYR A 124 SITE 2 AC4 11 GLU A 130 ASN A 132 SER A 202 ASN A 205 SITE 3 AC4 11 HIS A 206 TYR A 257 PHE A 259 CRYST1 103.439 103.439 112.202 90.00 90.00 120.00 P 61 6 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 0.009668 0.005582 0.000000 0.00000 SCALE2 0.000000 0.011163 0.000000 0.00000 SCALE3 0.000000 0.000000 0.008912 0.00000