PDB Short entry for 3MEK HEADER TRANSFERASE 31-MAR-10 3MEK TITLE CRYSTAL STRUCTURE OF HUMAN HISTONE-LYSINE N-METHYLTRANSFERASE SMYD3 IN TITLE 2 COMPLEX WITH S-ADENOSYL-L-METHIONINE 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)-V2R-PRARE2; SOURCE 9 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 10 EXPRESSION_SYSTEM_PLASMID: PET28-MHL KEYWDS HISTONE METHYLTRANSFERASE, SET AND MYND DOMAIN-CONTAINING PROTEIN 3, KEYWDS 2 ZINC FINGER MYND DOMAIN-CONTAINING PROTEIN 1, HISTONE H3, DI- KEYWDS 3 METHYLATION, TRI-METHYLATION, TRANSCRIPTIONAL ACTIVATION, DNA- KEYWDS 4 BINDING, MYND-TYPE ZINC FINGER, SET DOMAIN, CHROMATIN MODIFICATION, KEYWDS 5 ALTERNATIVE SPLICING, CHROMATIN REGULATOR, CYTOPLASM, METAL-BINDING, KEYWDS 6 METHYLTRANSFERASE, NUCLEUS, S-ADENOSYL-L-METHIONINE, TRANSFERASE, KEYWDS 7 ZINC, ZINC-FINGER, STRUCTURAL GENOMICS, STRUCTURAL GENOMICS KEYWDS 8 CONSORTIUM, SGC EXPDTA X-RAY DIFFRACTION AUTHOR R.LAM,L.DOMBROVSKI,Y.LI,C.BOUNTRA,J.WEIGELT,C.H.ARROWSMITH, AUTHOR 2 A.M.EDWARDS,A.BOCHKAREV,J.MIN,H.WU,STRUCTURAL GENOMICS CONSORTIUM AUTHOR 3 (SGC) REVDAT 2 08-NOV-17 3MEK 1 REMARK REVDAT 1 14-APR-10 3MEK 0 JRNL AUTH R.LAM,L.DOMBROVSKI,Y.LI,C.BOUNTRA,J.WEIGELT,C.H.ARROWSMITH, JRNL AUTH 2 A.M.EDWARDS,A.BOCHKAREV,J.MIN,H.WU JRNL TITL CRYSTAL STRUCTURE OF HUMAN HISTONE-LYSINE JRNL TITL 2 N-METHYLTRANSFERASE SMYD3 IN COMPLEX WITH JRNL TITL 3 S-ADENOSYL-L-METHIONINE JRNL REF TO BE PUBLISHED JRNL REFN REMARK 2 REMARK 2 RESOLUTION. 2.10 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC REFMAC_5.5.0109 REMARK 3 AUTHORS : MURSHUDOV,VAGIN,DODSON REMARK 3 REMARK 3 REFINEMENT TARGET : NULL REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.10 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 44.70 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 99.7 REMARK 3 NUMBER OF REFLECTIONS : 26172 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) : 0.176 REMARK 3 R VALUE (WORKING SET) : 0.174 REMARK 3 FREE R VALUE : 0.208 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.074 REMARK 3 FREE R VALUE TEST SET COUNT : 1328 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) : 2.10 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.15 REMARK 3 REFLECTION IN BIN (WORKING SET) : 1716 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 96.02 REMARK 3 BIN R VALUE (WORKING SET) : 0.1870 REMARK 3 BIN FREE R VALUE SET COUNT : 94 REMARK 3 BIN FREE R VALUE : 0.2480 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 3339 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 30 REMARK 3 SOLVENT ATOMS : 175 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 18.78 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -0.02700 REMARK 3 B22 (A**2) : 0.02800 REMARK 3 B33 (A**2) : -0.00100 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): 0.215 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.168 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 : 0.946 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.921 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 3451 ; 0.011 ; 0.022 REMARK 3 BOND LENGTHS OTHERS (A): NULL ; NULL ; NULL REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 4666 ; 1.272 ; 1.984 REMARK 3 BOND ANGLES OTHERS (DEGREES): NULL ; NULL ; NULL REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 430 ; 5.340 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 157 ;33.040 ;24.013 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 626 ;13.559 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 26 ;17.047 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 519 ; 0.087 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 2585 ; 0.005 ; 0.021 REMARK 3 GENERAL PLANES OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): 1567 ; 0.195 ; 0.200 REMARK 3 NON-BONDED CONTACTS OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION REFINED ATOMS (A): 2402 ; 0.298 ; 0.200 REMARK 3 NON-BONDED TORSION OTHERS (A): NULL ; NULL ; NULL REMARK 3 H-BOND (X...Y) REFINED ATOMS (A): 195 ; 0.107 ; 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): 35 ; 0.166 ; 0.200 REMARK 3 SYMMETRY VDW OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY H-BOND REFINED ATOMS (A): 12 ; 0.126 ; 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): 2129 ; 0.628 ; 1.500 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 3428 ; 1.261 ; 2.000 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 1322 ; 2.321 ; 3.000 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 1234 ; 3.853 ; 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 : 1 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 3 A 425 REMARK 3 ORIGIN FOR THE GROUP (A): 12.2080 32.5920 12.9020 REMARK 3 T TENSOR REMARK 3 T11: 0.0082 T22: 0.0092 REMARK 3 T33: 0.0184 T12: -0.0053 REMARK 3 T13: -0.0015 T23: 0.0014 REMARK 3 L TENSOR REMARK 3 L11: 0.1889 L22: 0.3384 REMARK 3 L33: 0.4733 L12: -0.1144 REMARK 3 L13: -0.1562 L23: 0.1611 REMARK 3 S TENSOR REMARK 3 S11: 0.0155 S12: 0.0002 S13: 0.0098 REMARK 3 S21: -0.0274 S22: -0.0026 S23: -0.0124 REMARK 3 S31: -0.0542 S32: 0.0211 S33: -0.0129 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : BABINET MODEL PLUS 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 3MEK COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 01-APR-10. REMARK 100 THE DEPOSITION ID IS D_1000058446. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 17-FEB-10 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 8.0 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : APS REMARK 200 BEAMLINE : 19-ID REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.97935 REMARK 200 MONOCHROMATOR : DOUBLE-CRYSTAL MONOCHROMATOR REMARK 200 OPTICS : ROSENBAUM-ROCK HIGH- RESOLUTION REMARK 200 DOUBLE-CRYSTAL MONOCHROMATOR REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 315 REMARK 200 INTENSITY-INTEGRATION SOFTWARE : DENZO, HKL-3000 REMARK 200 DATA SCALING SOFTWARE : SCALEPACK, HKL-3000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 26234 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.100 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 (%) : 100.0 REMARK 200 DATA REDUNDANCY : 7.500 REMARK 200 R MERGE (I) : 0.14500 REMARK 200 R SYM (I) : NULL REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 6.4000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.10 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.18 REMARK 200 COMPLETENESS FOR SHELL (%) : 100.0 REMARK 200 DATA REDUNDANCY IN SHELL : 7.20 REMARK 200 R MERGE FOR SHELL (I) : 0.42300 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: SAD REMARK 200 SOFTWARE USED: SHARP, DM 6.1 REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 43.25 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.17 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 20% PEG3350, 0.2M MG FORMATE, PH 8.0, REMARK 280 VAPOR DIFFUSION, SITTING 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 30.40450 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 54.05100 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 32.96150 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 54.05100 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 30.40450 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 32.96150 REMARK 290 SMTRY3 4 0.000000 0.000000 -1.000000 0.00000 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 GLY A 0 REMARK 465 MSE A 1 REMARK 465 GLU A 2 REMARK 465 ARG A 426 REMARK 465 ALA A 427 REMARK 465 SER A 428 REMARK 470 REMARK 470 MISSING ATOM REMARK 470 THE FOLLOWING RESIDUES HAVE MISSING ATOMS (M=MODEL NUMBER; REMARK 470 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; REMARK 470 I=INSERTION CODE): REMARK 470 M RES CSSEQI ATOMS REMARK 470 ARG A 25 CG CD NE CZ NH1 NH2 REMARK 470 GLU A 57 CG CD OE1 OE2 REMARK 470 LYS A 58 CG CD CE NZ REMARK 470 LYS A 88 CG CD CE NZ REMARK 470 LYS A 94 CG CD CE NZ REMARK 470 ARG A 96 CG CD NE CZ NH1 NH2 REMARK 470 GLU A 138 CG CD OE1 OE2 REMARK 470 GLN A 281 CG CD OE1 NE2 REMARK 470 LYS A 292 CG CD CE NZ REMARK 470 LYS A 391 CG CD CE NZ REMARK 470 ASP A 422 CG OD1 OD2 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 16.83 -140.60 REMARK 500 TYR A 124 134.01 -171.45 REMARK 500 LYS A 271 -11.93 82.85 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 500 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HIS A 83 NE2 REMARK 620 2 CYS A 87 SG 107.4 REMARK 620 3 CYS A 62 SG 113.8 108.5 REMARK 620 4 CYS A 65 SG 103.7 112.3 111.1 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 ZN A 502 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS A 208 SG REMARK 620 2 CYS A 261 SG 113.5 REMARK 620 3 CYS A 263 SG 109.0 106.7 REMARK 620 4 CYS A 266 SG 101.3 115.0 111.3 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 ZN A 501 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS A 75 SG REMARK 620 2 CYS A 49 SG 107.4 REMARK 620 3 CYS A 52 SG 117.6 107.9 REMARK 620 4 CYS A 71 SG 104.7 110.6 108.6 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 500 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ZN A 501 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ZN A 502 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SAM A 510 REMARK 999 REMARK 999 SEQUENCE REMARK 999 AUTHORS STATE THAT THEY BASED THE TEMPLATE FOR SMYD3 ON THE MGC REMARK 999 CLONE (ACCESSION BC031010, VERSION BC031010.1, GI:21410973) DBREF 3MEK A 1 428 UNP Q9H7B4 SMYD3_HUMAN 1 428 SEQADV 3MEK GLY A 0 UNP Q9H7B4 EXPRESSION TAG SEQADV 3MEK ASN A 13 UNP Q9H7B4 LYS 13 SEE REMARK 999 SEQADV 3MEK ARG A 140 UNP Q9H7B4 LYS 140 SEE REMARK 999 SEQRES 1 A 429 GLY MSE GLU PRO LEU LYS VAL GLU LYS PHE ALA THR ALA SEQRES 2 A 429 ASN ARG GLY ASN GLY LEU ARG ALA VAL THR PRO LEU ARG SEQRES 3 A 429 PRO GLY GLU LEU LEU PHE ARG SER ASP PRO LEU ALA TYR SEQRES 4 A 429 THR VAL CYS LYS GLY SER ARG GLY VAL VAL CYS ASP ARG SEQRES 5 A 429 CYS LEU LEU GLY LYS GLU LYS LEU MSE ARG CYS SER GLN SEQRES 6 A 429 CYS ARG VAL ALA LYS TYR CYS SER ALA LYS CYS GLN LYS SEQRES 7 A 429 LYS ALA TRP PRO ASP HIS LYS ARG GLU CYS LYS CYS LEU SEQRES 8 A 429 LYS SER CYS LYS PRO ARG TYR PRO PRO ASP SER VAL ARG SEQRES 9 A 429 LEU LEU GLY ARG VAL VAL PHE LYS LEU MSE ASP GLY ALA SEQRES 10 A 429 PRO SER GLU SER GLU LYS LEU TYR SER PHE TYR ASP LEU SEQRES 11 A 429 GLU SER ASN ILE ASN LYS LEU THR GLU ASP ARG LYS GLU SEQRES 12 A 429 GLY LEU ARG GLN LEU VAL MSE THR PHE GLN HIS PHE MSE SEQRES 13 A 429 ARG GLU GLU ILE GLN ASP ALA SER GLN LEU PRO PRO ALA SEQRES 14 A 429 PHE ASP LEU PHE GLU ALA PHE ALA LYS VAL ILE CYS ASN SEQRES 15 A 429 SER PHE THR ILE CYS ASN ALA GLU MSE GLN GLU VAL GLY SEQRES 16 A 429 VAL GLY LEU TYR PRO SER ILE SER LEU LEU ASN HIS SER SEQRES 17 A 429 CYS ASP PRO ASN CYS SER ILE VAL PHE ASN GLY PRO HIS SEQRES 18 A 429 LEU LEU LEU ARG ALA VAL ARG ASP ILE GLU VAL GLY GLU SEQRES 19 A 429 GLU LEU THR ILE CYS TYR LEU ASP MSE LEU MSE THR SER SEQRES 20 A 429 GLU GLU ARG ARG LYS GLN LEU ARG ASP GLN TYR CYS PHE SEQRES 21 A 429 GLU CYS ASP CYS PHE ARG CYS GLN THR GLN ASP LYS ASP SEQRES 22 A 429 ALA ASP MSE LEU THR GLY ASP GLU GLN VAL TRP LYS GLU SEQRES 23 A 429 VAL GLN GLU SER LEU LYS LYS ILE GLU GLU LEU LYS ALA SEQRES 24 A 429 HIS TRP LYS TRP GLU GLN VAL LEU ALA MSE CYS GLN ALA SEQRES 25 A 429 ILE ILE SER SER ASN SER GLU ARG LEU PRO ASP ILE ASN SEQRES 26 A 429 ILE TYR GLN LEU LYS VAL LEU ASP CYS ALA MSE ASP ALA SEQRES 27 A 429 CYS ILE ASN LEU GLY LEU LEU GLU GLU ALA LEU PHE TYR SEQRES 28 A 429 GLY THR ARG THR MSE GLU PRO TYR ARG ILE PHE PHE PRO SEQRES 29 A 429 GLY SER HIS PRO VAL ARG GLY VAL GLN VAL MSE LYS VAL SEQRES 30 A 429 GLY LYS LEU GLN LEU HIS GLN GLY MSE PHE PRO GLN ALA SEQRES 31 A 429 MSE LYS ASN LEU ARG LEU ALA PHE ASP ILE MSE ARG VAL SEQRES 32 A 429 THR HIS GLY ARG GLU HIS SER LEU ILE GLU ASP LEU ILE SEQRES 33 A 429 LEU LEU LEU GLU GLU CYS ASP ALA ASN ILE ARG ALA SER MODRES 3MEK MSE A 60 MET SELENOMETHIONINE MODRES 3MEK MSE A 113 MET SELENOMETHIONINE MODRES 3MEK MSE A 149 MET SELENOMETHIONINE MODRES 3MEK MSE A 155 MET SELENOMETHIONINE MODRES 3MEK MSE A 190 MET SELENOMETHIONINE MODRES 3MEK MSE A 242 MET SELENOMETHIONINE MODRES 3MEK MSE A 244 MET SELENOMETHIONINE MODRES 3MEK MSE A 275 MET SELENOMETHIONINE MODRES 3MEK MSE A 308 MET SELENOMETHIONINE MODRES 3MEK MSE A 335 MET SELENOMETHIONINE MODRES 3MEK MSE A 355 MET SELENOMETHIONINE MODRES 3MEK MSE A 374 MET SELENOMETHIONINE MODRES 3MEK MSE A 385 MET SELENOMETHIONINE MODRES 3MEK MSE A 390 MET SELENOMETHIONINE MODRES 3MEK MSE A 400 MET SELENOMETHIONINE HET MSE A 60 8 HET MSE A 113 8 HET MSE A 149 8 HET MSE A 155 8 HET MSE A 190 8 HET MSE A 242 8 HET MSE A 244 8 HET MSE A 275 8 HET MSE A 308 8 HET MSE A 335 8 HET MSE A 355 8 HET MSE A 374 8 HET MSE A 385 8 HET MSE A 390 8 HET MSE A 400 8 HET ZN A 500 1 HET ZN A 501 1 HET ZN A 502 1 HET SAM A 510 27 HETNAM MSE SELENOMETHIONINE HETNAM ZN ZINC ION HETNAM SAM S-ADENOSYLMETHIONINE FORMUL 1 MSE 15(C5 H11 N O2 SE) FORMUL 2 ZN 3(ZN 2+) FORMUL 5 SAM C15 H22 N6 O5 S FORMUL 6 HOH *175(H2 O) HELIX 1 1 SER A 72 SER A 92 1 21 HELIX 2 2 PRO A 99 GLY A 115 1 17 HELIX 3 3 SER A 118 LYS A 122 5 5 HELIX 4 4 SER A 125 LEU A 129 5 5 HELIX 5 5 ASN A 132 LEU A 136 5 5 HELIX 6 6 THR A 137 MSE A 155 1 19 HELIX 7 7 ASP A 161 LEU A 165 5 5 HELIX 8 8 ASP A 170 SER A 182 1 13 HELIX 9 9 SER A 200 LEU A 204 5 5 HELIX 10 10 THR A 245 CYS A 258 1 14 HELIX 11 11 CYS A 263 THR A 268 1 6 HELIX 12 12 LYS A 271 LEU A 276 1 6 HELIX 13 13 ASP A 279 HIS A 299 1 21 HELIX 14 14 LYS A 301 SER A 314 1 14 HELIX 15 15 ASN A 324 GLY A 342 1 19 HELIX 16 16 LEU A 343 PHE A 362 1 20 HELIX 17 17 HIS A 366 GLN A 383 1 18 HELIX 18 18 MSE A 385 HIS A 404 1 20 HELIX 19 19 HIS A 408 ASN A 424 1 17 SHEET 1 A 4 VAL A 6 ALA A 10 0 SHEET 2 A 4 ASN A 16 ALA A 20 -1 O GLY A 17 N PHE A 9 SHEET 3 A 4 GLU A 234 ILE A 237 -1 O LEU A 235 N LEU A 18 SHEET 4 A 4 ASN A 205 HIS A 206 1 N ASN A 205 O ILE A 237 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 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 VAL A 195 N THR A 39 SHEET 3 C 3 PHE A 183 CYS A 186 -1 N ILE A 185 O VAL A 193 SHEET 1 D 2 MSE A 60 ARG A 61 0 SHEET 2 D 2 LYS A 69 TYR A 70 -1 O TYR A 70 N MSE A 60 LINK C LEU A 59 N MSE A 60 1555 1555 1.33 LINK C MSE A 60 N ARG A 61 1555 1555 1.32 LINK C LEU A 112 N MSE A 113 1555 1555 1.32 LINK C MSE A 113 N ASP A 114 1555 1555 1.33 LINK C VAL A 148 N MSE A 149 1555 1555 1.33 LINK C MSE A 149 N THR A 150 1555 1555 1.34 LINK C PHE A 154 N MSE A 155 1555 1555 1.33 LINK C MSE A 155 N ARG A 156 1555 1555 1.34 LINK C GLU A 189 N MSE A 190 1555 1555 1.33 LINK C MSE A 190 N GLN A 191 1555 1555 1.33 LINK C ASP A 241 N MSE A 242 1555 1555 1.33 LINK C MSE A 242 N LEU A 243 1555 1555 1.33 LINK C LEU A 243 N MSE A 244 1555 1555 1.33 LINK C MSE A 244 N THR A 245 1555 1555 1.33 LINK C ASP A 274 N MSE A 275 1555 1555 1.33 LINK C MSE A 275 N LEU A 276 1555 1555 1.34 LINK C ALA A 307 N MSE A 308 1555 1555 1.33 LINK C MSE A 308 N CYS A 309 1555 1555 1.34 LINK C ALA A 334 N MSE A 335 1555 1555 1.32 LINK C MSE A 335 N ASP A 336 1555 1555 1.33 LINK C THR A 354 N MSE A 355 1555 1555 1.34 LINK C MSE A 355 N GLU A 356 1555 1555 1.32 LINK C VAL A 373 N MSE A 374 1555 1555 1.33 LINK C MSE A 374 N LYS A 375 1555 1555 1.33 LINK C GLY A 384 N MSE A 385 1555 1555 1.33 LINK C MSE A 385 N PHE A 386 1555 1555 1.33 LINK C ALA A 389 N MSE A 390 1555 1555 1.34 LINK C ILE A 399 N MSE A 400 1555 1555 1.33 LINK C MSE A 400 N ARG A 401 1555 1555 1.33 LINK NE2 HIS A 83 ZN ZN A 500 1555 1555 2.08 LINK SG CYS A 87 ZN ZN A 500 1555 1555 2.26 LINK SG CYS A 208 ZN ZN A 502 1555 1555 2.28 LINK SG CYS A 62 ZN ZN A 500 1555 1555 2.29 LINK SG CYS A 75 ZN ZN A 501 1555 1555 2.30 LINK SG CYS A 65 ZN ZN A 500 1555 1555 2.31 LINK SG CYS A 49 ZN ZN A 501 1555 1555 2.33 LINK SG CYS A 261 ZN ZN A 502 1555 1555 2.33 LINK SG CYS A 263 ZN ZN A 502 1555 1555 2.34 LINK SG CYS A 266 ZN ZN A 502 1555 1555 2.35 LINK SG CYS A 52 ZN ZN A 501 1555 1555 2.38 LINK SG CYS A 71 ZN ZN A 501 1555 1555 2.38 LINK C MSE A 390 N LYS A 391 1555 1555 1.33 CISPEP 1 LYS A 94 PRO A 95 0 4.24 SITE 1 AC1 4 CYS A 62 CYS A 65 HIS A 83 CYS A 87 SITE 1 AC2 4 CYS A 49 CYS A 52 CYS A 71 CYS A 75 SITE 1 AC3 4 CYS A 208 CYS A 261 CYS A 263 CYS A 266 SITE 1 AC4 20 ARG A 14 ASN A 16 TYR A 124 GLU A 130 SITE 2 AC4 20 ASN A 132 ASN A 181 SER A 202 LEU A 204 SITE 3 AC4 20 ASN A 205 HIS A 206 TYR A 239 TYR A 257 SITE 4 AC4 20 PHE A 259 HOH A 438 HOH A 458 HOH A 519 SITE 5 AC4 20 HOH A 562 HOH A 563 HOH A 571 HOH A 576 CRYST1 60.809 65.923 108.102 90.00 90.00 90.00 P 21 21 21 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 0.016445 0.000000 0.000000 0.00000 SCALE2 0.000000 0.015169 0.000000 0.00000 SCALE3 0.000000 0.000000 0.009251 0.00000