HEADER ONCOPROTEIN 13-JAN-21 7BJ1 TITLE CRYSTAL STRUCTURE OF SMYD3 WITH DIPERODON S ENANTIOMER BOUND TO TITLE 2 ALLOSTERIC SITE COMPND MOL_ID: 1; COMPND 2 MOLECULE: HISTONE-LYSINE N-METHYLTRANSFERASE SMYD3; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: SET AND MYND DOMAIN-CONTAINING PROTEIN 3,ZINC FINGER MYND COMPND 5 DOMAIN-CONTAINING PROTEIN 1; COMPND 6 EC: 2.1.1.354; COMPND 7 ENGINEERED: YES; COMPND 8 MUTATION: 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 BL21(DE3); SOURCE 7 EXPRESSION_SYSTEM_TAXID: 469008 KEYWDS METHYLTRANSFERASE, COMPLEX, INHIBITOR, ONCOPROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR V.O.TALIBOV,D.CEDERFELT,D.DOBRITZSCH,U.H.DANIELSON REVDAT 5 31-JAN-24 7BJ1 1 REMARK REVDAT 4 06-OCT-21 7BJ1 1 AUTHOR JRNL REVDAT 3 17-MAR-21 7BJ1 1 OBSLTE SPRSDE REVDAT 2 10-MAR-21 7BJ1 1 OBSLTE REVDAT 1 03-MAR-21 7BJ1 0 SPRSDE 21-MAR-21 7BJ1 6Z2R JRNL AUTH V.O.TALIBOV,E.FABINI,E.A.FITZGERALD,D.TEDESCO,D.CEDERFELDT, JRNL AUTH 2 M.J.TALU,M.M.RACHMAN,F.MIHALIC,E.MANONI,M.NALDI,P.SANESE, JRNL AUTH 3 G.FORTE,X.BARRIL,C.SIMONE,M.BARTOLINI,D.DOBRITZSCH, JRNL AUTH 4 U.H.DANIELSON JRNL TITL DISCOVERY OF AN ALLOSTERIC LIGAND BINDING SITE IN SMYD3 JRNL TITL 2 LYSINE METHYLTRANSFERASE JRNL REF CHEMBIOCHEM V. 22 1597 2021 JRNL REFN ESSN 1439-7633 JRNL DOI 10.1002/CBIC.202000736 REMARK 2 REMARK 2 RESOLUTION. 1.61 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.8.0131 REMARK 3 AUTHORS : MURSHUDOV,SKUBAK,LEBEDEV,PANNU,STEINER, REMARK 3 : NICHOLLS,WINN,LONG,VAGIN REMARK 3 REMARK 3 REFINEMENT TARGET : GEOSTD + MONOMER LIBRARY + CDL V1.2 REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.61 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 44.78 REMARK 3 DATA CUTOFF (SIGMA(F)) : 1.350 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.8 REMARK 3 NUMBER OF REFLECTIONS : 56641 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 CROSS-VALIDATION METHOD : FREE R-VALUE REMARK 3 FREE R VALUE TEST SET SELECTION : NULL REMARK 3 R VALUE (WORKING + TEST SET) : 0.173 REMARK 3 R VALUE (WORKING SET) : 0.172 REMARK 3 FREE R VALUE : 0.210 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.820 REMARK 3 FREE R VALUE TEST SET COUNT : 2730 REMARK 3 REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN. REMARK 3 TOTAL NUMBER OF BINS USED : NULL REMARK 3 BIN RESOLUTION RANGE HIGH (A) : 1.61 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.64 REMARK 3 REFLECTION IN BIN (WORKING SET) : 2750 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 98.98 REMARK 3 BIN R VALUE (WORKING SET) : 0.3919 REMARK 3 BIN FREE R VALUE SET COUNT : 151 REMARK 3 BIN FREE R VALUE : 0.4599 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 3408 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 79 REMARK 3 SOLVENT ATOMS : 523 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 30.10 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : NULL REMARK 3 B22 (A**2) : NULL REMARK 3 B33 (A**2) : NULL REMARK 3 B12 (A**2) : NULL REMARK 3 B13 (A**2) : NULL REMARK 3 B23 (A**2) : NULL 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): NULL REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.246 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 : NULL REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : NULL REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 BOND LENGTHS OTHERS (A): NULL ; NULL ; NULL REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): NULL ; NULL ; NULL REMARK 3 BOND ANGLES OTHERS (DEGREES): NULL ; NULL ; NULL REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): NULL ; NULL ; NULL REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): NULL ; NULL ; NULL REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): NULL ; NULL ; NULL REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): NULL ; NULL ; NULL REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): NULL ; NULL ; NULL REMARK 3 GENERAL PLANES REFINED ATOMS (A): NULL ; NULL ; NULL 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): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): NULL ; NULL ; NULL 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 : FLAT BULK SOLVENT MODEL REMARK 3 PARAMETERS FOR MASK CALCULATION REMARK 3 VDW PROBE RADIUS : 1.11 REMARK 3 ION PROBE RADIUS : NULL REMARK 3 SHRINKAGE RADIUS : 0.90 REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 7BJ1 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 14-JAN-21. REMARK 100 THE DEPOSITION ID IS D_1292113467. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 19-JUN-18 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 8.25 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : ESRF REMARK 200 BEAMLINE : ID29 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.976 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS PILATUS 6M-F REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS B. 20180126 REMARK 200 DATA SCALING SOFTWARE : AIMLESS 0.7.1 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 56743 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.610 REMARK 200 RESOLUTION RANGE LOW (A) : 56.240 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.9 REMARK 200 DATA REDUNDANCY : 5.100 REMARK 200 R MERGE (I) : 0.06700 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 12.3000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.61 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.67 REMARK 200 COMPLETENESS FOR SHELL (%) : 99.8 REMARK 200 DATA REDUNDANCY IN SHELL : 4.80 REMARK 200 R MERGE FOR SHELL (I) : 1.52800 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: PHASER REMARK 200 STARTING MODEL: 5CCL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 43.62 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.18 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: PROTEIN: 50 MM TRIS, 150 MM NACL, 1 MM REMARK 280 (S)-DIPERODON, 10% DMSO, PH 8.0; RESERVOIR: 100 MM TRIS, 50 MM REMARK 280 MAGNESIUM ACETATE, 11% PEG3350, PH 8.25, VAPOR DIFFUSION, REMARK 280 HANGING DROP, TEMPERATURE 293K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 21 21 21 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X+1/2,-Y,Z+1/2 REMARK 290 3555 -X,Y+1/2,-Z+1/2 REMARK 290 4555 X+1/2,-Y+1/2,-Z REMARK 290 REMARK 290 WHERE NNN -> OPERATOR NUMBER REMARK 290 MMM -> TRANSLATION VECTOR REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY TRANSFORMATIONS REMARK 290 THE FOLLOWING TRANSFORMATIONS OPERATE ON THE ATOM/HETATM REMARK 290 RECORDS IN THIS ENTRY TO PRODUCE CRYSTALLOGRAPHICALLY REMARK 290 RELATED MOLECULES. REMARK 290 SMTRY1 1 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 1 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 1 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 2 -1.000000 0.000000 0.000000 30.45450 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 53.63850 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 33.02500 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 53.63850 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 30.45450 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 33.02500 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 TOTAL BURIED SURFACE AREA: 780 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 20000 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -1.0 KCAL/MOL 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 -2 REMARK 465 SER A -1 REMARK 465 HIS A 0 REMARK 465 MET A 1 REMARK 465 GLU A 2 REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CLOSE CONTACTS IN SAME ASYMMETRIC UNIT REMARK 500 REMARK 500 THE FOLLOWING ATOMS ARE IN CLOSE CONTACT. REMARK 500 REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI DISTANCE REMARK 500 OE2 GLU A 280 O HOH A 601 2.10 REMARK 500 O HOH A 950 O HOH A 1006 2.16 REMARK 500 O HOH A 941 O HOH A 1074 2.18 REMARK 500 O HOH A 689 O HOH A 732 2.19 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CLOSE CONTACTS REMARK 500 REMARK 500 THE FOLLOWING ATOMS THAT ARE RELATED BY CRYSTALLOGRAPHIC REMARK 500 SYMMETRY ARE IN CLOSE CONTACT. AN ATOM LOCATED WITHIN 0.15 REMARK 500 ANGSTROMS OF A SYMMETRY RELATED ATOM IS ASSUMED TO BE ON A REMARK 500 SPECIAL POSITION AND IS, THEREFORE, LISTED IN REMARK 375 REMARK 500 INSTEAD OF REMARK 500. ATOMS WITH NON-BLANK ALTERNATE REMARK 500 LOCATION INDICATORS ARE NOT INCLUDED IN THE CALCULATIONS. REMARK 500 REMARK 500 DISTANCE CUTOFF: REMARK 500 2.2 ANGSTROMS FOR CONTACTS NOT INVOLVING HYDROGEN ATOMS REMARK 500 1.6 ANGSTROMS FOR CONTACTS INVOLVING HYDROGEN ATOMS REMARK 500 REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI SSYMOP DISTANCE REMARK 500 O HOH A 760 O HOH A 982 4455 2.16 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: TORSION ANGLES REMARK 500 REMARK 500 TORSION ANGLES OUTSIDE THE EXPECTED RAMACHANDRAN REGIONS: REMARK 500 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 500 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 STANDARD TABLE: REMARK 500 FORMAT:(10X,I3,1X,A3,1X,A1,I4,A1,4X,F7.2,3X,F7.2) REMARK 500 REMARK 500 EXPECTED VALUES: GJ KLEYWEGT AND TA JONES (1996). PHI/PSI- REMARK 500 CHOLOGY: RAMACHANDRAN REVISITED. STRUCTURE 4, 1395 - 1400 REMARK 500 REMARK 500 M RES CSSEQI PSI PHI REMARK 500 ASN A 13 21.39 -143.73 REMARK 500 ARG A 14 39.73 -140.11 REMARK 500 LYS A 84 -62.52 -29.75 REMARK 500 LYS A 88 -61.84 -27.83 REMARK 500 CYS A 93 31.10 -98.21 REMARK 500 TYR A 124 139.17 -171.92 REMARK 500 LYS A 271 -6.08 77.63 REMARK 500 ALA A 427 20.17 -72.94 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 504 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS A 49 SG REMARK 620 2 CYS A 52 SG 105.9 REMARK 620 3 CYS A 71 SG 114.5 107.6 REMARK 620 4 CYS A 75 SG 108.9 115.6 104.6 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 ZN A 505 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS A 62 SG REMARK 620 2 CYS A 65 SG 110.7 REMARK 620 3 HIS A 83 NE2 113.9 101.4 REMARK 620 4 CYS A 87 SG 110.5 110.8 109.2 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 ZN A 503 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS A 208 SG REMARK 620 2 CYS A 261 SG 113.9 REMARK 620 3 CYS A 263 SG 106.2 109.3 REMARK 620 4 CYS A 266 SG 100.7 114.7 111.5 REMARK 620 N 1 2 3 DBREF 7BJ1 A 1 428 UNP Q9H7B4 SMYD3_HUMAN 1 428 SEQADV 7BJ1 GLY A -2 UNP Q9H7B4 EXPRESSION TAG SEQADV 7BJ1 SER A -1 UNP Q9H7B4 EXPRESSION TAG SEQADV 7BJ1 HIS A 0 UNP Q9H7B4 EXPRESSION TAG SEQADV 7BJ1 ASN A 13 UNP Q9H7B4 LYS 13 ENGINEERED MUTATION SEQADV 7BJ1 ARG A 140 UNP Q9H7B4 LYS 140 ENGINEERED MUTATION SEQRES 1 A 431 GLY SER HIS MET GLU PRO LEU LYS VAL GLU LYS PHE ALA SEQRES 2 A 431 THR ALA ASN ARG GLY ASN GLY LEU ARG ALA VAL THR PRO SEQRES 3 A 431 LEU ARG PRO GLY GLU LEU LEU PHE ARG SER ASP PRO LEU SEQRES 4 A 431 ALA TYR THR VAL CYS LYS GLY SER ARG GLY VAL VAL CYS SEQRES 5 A 431 ASP ARG CYS LEU LEU GLY LYS GLU LYS LEU MET ARG CYS SEQRES 6 A 431 SER GLN CYS ARG VAL ALA LYS TYR CYS SER ALA LYS CYS SEQRES 7 A 431 GLN LYS LYS ALA TRP PRO ASP HIS LYS ARG GLU CYS LYS SEQRES 8 A 431 CYS LEU LYS SER CYS LYS PRO ARG TYR PRO PRO ASP SER SEQRES 9 A 431 VAL ARG LEU LEU GLY ARG VAL VAL PHE LYS LEU MET ASP SEQRES 10 A 431 GLY ALA PRO SER GLU SER GLU LYS LEU TYR SER PHE TYR SEQRES 11 A 431 ASP LEU GLU SER ASN ILE ASN LYS LEU THR GLU ASP ARG SEQRES 12 A 431 LYS GLU GLY LEU ARG GLN LEU VAL MET THR PHE GLN HIS SEQRES 13 A 431 PHE MET ARG GLU GLU ILE GLN ASP ALA SER GLN LEU PRO SEQRES 14 A 431 PRO ALA PHE ASP LEU PHE GLU ALA PHE ALA LYS VAL ILE SEQRES 15 A 431 CYS ASN SER PHE THR ILE CYS ASN ALA GLU MET GLN GLU SEQRES 16 A 431 VAL GLY VAL GLY LEU TYR PRO SER ILE SER LEU LEU ASN SEQRES 17 A 431 HIS SER CYS ASP PRO ASN CYS SER ILE VAL PHE ASN GLY SEQRES 18 A 431 PRO HIS LEU LEU LEU ARG ALA VAL ARG ASP ILE GLU VAL SEQRES 19 A 431 GLY GLU GLU LEU THR ILE CYS TYR LEU ASP MET LEU MET SEQRES 20 A 431 THR SER GLU GLU ARG ARG LYS GLN LEU ARG ASP GLN TYR SEQRES 21 A 431 CYS PHE GLU CYS ASP CYS PHE ARG CYS GLN THR GLN ASP SEQRES 22 A 431 LYS ASP ALA ASP MET LEU THR GLY ASP GLU GLN VAL TRP SEQRES 23 A 431 LYS GLU VAL GLN GLU SER LEU LYS LYS ILE GLU GLU LEU SEQRES 24 A 431 LYS ALA HIS TRP LYS TRP GLU GLN VAL LEU ALA MET CYS SEQRES 25 A 431 GLN ALA ILE ILE SER SER ASN SER GLU ARG LEU PRO ASP SEQRES 26 A 431 ILE ASN ILE TYR GLN LEU LYS VAL LEU ASP CYS ALA MET SEQRES 27 A 431 ASP ALA CYS ILE ASN LEU GLY LEU LEU GLU GLU ALA LEU SEQRES 28 A 431 PHE TYR GLY THR ARG THR MET GLU PRO TYR ARG ILE PHE SEQRES 29 A 431 PHE PRO GLY SER HIS PRO VAL ARG GLY VAL GLN VAL MET SEQRES 30 A 431 LYS VAL GLY LYS LEU GLN LEU HIS GLN GLY MET PHE PRO SEQRES 31 A 431 GLN ALA MET LYS ASN LEU ARG LEU ALA PHE ASP ILE MET SEQRES 32 A 431 ARG VAL THR HIS GLY ARG GLU HIS SER LEU ILE GLU ASP SEQRES 33 A 431 LEU ILE LEU LEU LEU GLU GLU CYS ASP ALA ASN ILE ARG SEQRES 34 A 431 ALA SER HET SAM A 501 27 HET QKT A 502 29 HET ZN A 503 1 HET ZN A 504 1 HET ZN A 505 1 HET ACT A 506 4 HET ACT A 507 4 HET GOL A 508 6 HET GOL A 509 6 HETNAM SAM S-ADENOSYLMETHIONINE HETNAM QKT DIPERODON (S-ENANTIOMER) HETNAM ZN ZINC ION HETNAM ACT ACETATE ION HETNAM GOL GLYCEROL HETSYN GOL GLYCERIN; PROPANE-1,2,3-TRIOL FORMUL 2 SAM C15 H22 N6 O5 S FORMUL 3 QKT C22 H27 N3 O4 FORMUL 4 ZN 3(ZN 2+) FORMUL 7 ACT 2(C2 H3 O2 1-) FORMUL 9 GOL 2(C3 H8 O3) FORMUL 11 HOH *523(H2 O) HELIX 1 AA1 LYS A 42 ARG A 45 5 4 HELIX 2 AA2 SER A 72 CYS A 93 1 22 HELIX 3 AA3 PRO A 99 GLY A 115 1 17 HELIX 4 AA4 SER A 118 LYS A 122 5 5 HELIX 5 AA5 SER A 125 LEU A 129 5 5 HELIX 6 AA6 ASN A 132 LEU A 136 5 5 HELIX 7 AA7 THR A 137 MET A 155 1 19 HELIX 8 AA8 ASP A 161 LEU A 165 5 5 HELIX 9 AA9 ASP A 170 SER A 182 1 13 HELIX 10 AB1 SER A 200 LEU A 204 5 5 HELIX 11 AB2 THR A 245 CYS A 258 1 14 HELIX 12 AB3 CYS A 263 GLN A 269 1 7 HELIX 13 AB4 LYS A 271 LEU A 276 1 6 HELIX 14 AB5 ASP A 279 HIS A 299 1 21 HELIX 15 AB6 LYS A 301 SER A 314 1 14 HELIX 16 AB7 ASN A 324 GLY A 342 1 19 HELIX 17 AB8 LEU A 343 PHE A 362 1 20 HELIX 18 AB9 HIS A 366 GLN A 383 1 18 HELIX 19 AC1 MET A 385 HIS A 404 1 20 HELIX 20 AC2 HIS A 408 ALA A 427 1 20 SHEET 1 AA1 4 VAL A 6 ALA A 10 0 SHEET 2 AA1 4 ASN A 16 ALA A 20 -1 O GLY A 17 N PHE A 9 SHEET 3 AA1 4 GLU A 234 ILE A 237 -1 O LEU A 235 N LEU A 18 SHEET 4 AA1 4 ASN A 205 HIS A 206 1 N ASN A 205 O ILE A 237 SHEET 1 AA2 3 LEU A 29 SER A 33 0 SHEET 2 AA2 3 HIS A 220 ALA A 225 -1 O LEU A 223 N LEU A 30 SHEET 3 AA2 3 CYS A 212 ASN A 217 -1 N ASN A 217 O HIS A 220 SHEET 1 AA3 3 ALA A 37 VAL A 40 0 SHEET 2 AA3 3 GLU A 192 LEU A 197 -1 O LEU A 197 N ALA A 37 SHEET 3 AA3 3 PHE A 183 CYS A 186 -1 N PHE A 183 O GLY A 196 SHEET 1 AA4 2 MET A 60 ARG A 61 0 SHEET 2 AA4 2 LYS A 69 TYR A 70 -1 O TYR A 70 N MET A 60 LINK SG CYS A 49 ZN ZN A 504 1555 1555 2.37 LINK SG CYS A 52 ZN ZN A 504 1555 1555 2.33 LINK SG CYS A 62 ZN ZN A 505 1555 1555 2.29 LINK SG CYS A 65 ZN ZN A 505 1555 1555 2.32 LINK SG CYS A 71 ZN ZN A 504 1555 1555 2.29 LINK SG CYS A 75 ZN ZN A 504 1555 1555 2.29 LINK NE2 HIS A 83 ZN ZN A 505 1555 1555 2.12 LINK SG CYS A 87 ZN ZN A 505 1555 1555 2.35 LINK SG CYS A 208 ZN ZN A 503 1555 1555 2.37 LINK SG CYS A 261 ZN ZN A 503 1555 1555 2.34 LINK SG CYS A 263 ZN ZN A 503 1555 1555 2.30 LINK SG CYS A 266 ZN ZN A 503 1555 1555 2.33 CRYST1 60.909 66.050 107.277 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 0.016418 0.000000 0.000000 0.00000 SCALE2 0.000000 0.015140 0.000000 0.00000 SCALE3 0.000000 0.000000 0.009322 0.00000