HEADER TRANSFERASE/TRANSFERASE INHIBITOR 07-MAR-17 5V3H
TITLE CRYSTAL STRUCTURE OF SMYD2 WITH SAM AND EPZ033294
COMPND MOL_ID: 1;
COMPND 2 MOLECULE: N-LYSINE METHYLTRANSFERASE SMYD2;
COMPND 3 CHAIN: A;
COMPND 4 SYNONYM: HSKM-B,HISTONE METHYLTRANSFERASE SMYD2,LYSINE N-
COMPND 5 METHYLTRANSFERASE 3C,SET AND MYND DOMAIN-CONTAINING PROTEIN 2;
COMPND 6 EC: 2.1.1.-,2.1.1.43;
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: SMYD2, KMT3C;
SOURCE 6 EXPRESSION_SYSTEM: SPODOPTERA FRUGIPERDA;
SOURCE 7 EXPRESSION_SYSTEM_COMMON: FALL ARMYWORM;
SOURCE 8 EXPRESSION_SYSTEM_TAXID: 7108;
SOURCE 9 EXPRESSION_SYSTEM_VECTOR_TYPE: BACULOVIRUS;
SOURCE 10 EXPRESSION_SYSTEM_PLASMID: PFASTBACHTB-LIC
KEYWDS PROTEIN-INHIBITOR COMPLEX, PROTEIN LYSINE METHYLTRANSFERASE,
KEYWDS 2 TRANSFERASE-TRANSFERASE INHIBITOR COMPLEX
EXPDTA X-RAY DIFFRACTION
AUTHOR P.A.BORIACK-SJODIN
REVDAT 4 06-MAR-24 5V3H 1 REMARK
REVDAT 3 08-MAY-19 5V3H 1 JRNL
REVDAT 2 13-JUN-18 5V3H 1 TITLE
REVDAT 1 25-APR-18 5V3H 0
JRNL AUTH M.J.THOMENIUS,J.TOTMAN,D.HARVEY,L.H.MITCHELL,T.V.RIERA,
JRNL AUTH 2 K.COSMOPOULOS,A.R.GRASSIAN,C.KLAUS,M.FOLEY,E.A.ADMIRAND,
JRNL AUTH 3 H.JAHIC,C.MAJER,T.WIGLE,S.L.JACQUES,J.GUREASKO,D.BRACH,
JRNL AUTH 4 T.LINGARAJ,K.WEST,S.SMITH,N.RIOUX,N.J.WATERS,C.TANG,
JRNL AUTH 5 A.RAIMONDI,M.MUNCHHOF,J.E.MILLS,S.RIBICH,M.PORTER SCOTT,
JRNL AUTH 6 K.W.KUNTZ,W.P.JANZEN,M.MOYER,J.J.SMITH,R.CHESWORTH,
JRNL AUTH 7 R.A.COPELAND,P.A.BORIACK-SJODIN
JRNL TITL SMALL MOLECULE INHIBITORS AND CRISPR/CAS9 MUTAGENESIS
JRNL TITL 2 DEMONSTRATE THAT SMYD2 AND SMYD3 ACTIVITY ARE DISPENSABLE
JRNL TITL 3 FOR AUTONOMOUS CANCER CELL PROLIFERATION.
JRNL REF PLOS ONE V. 13 97372 2018
JRNL REFN ESSN 1932-6203
JRNL PMID 29856759
JRNL DOI 10.1371/JOURNAL.PONE.0197372
REMARK 2
REMARK 2 RESOLUTION. 2.69 ANGSTROMS.
REMARK 3
REMARK 3 REFINEMENT.
REMARK 3 PROGRAM : REFMAC 5.8.0155
REMARK 3 AUTHORS : MURSHUDOV,SKUBAK,LEBEDEV,PANNU,STEINER,
REMARK 3 : NICHOLLS,WINN,LONG,VAGIN
REMARK 3
REMARK 3 REFINEMENT TARGET : NULL
REMARK 3
REMARK 3 DATA USED IN REFINEMENT.
REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.69
REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 50.00
REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000
REMARK 3 COMPLETENESS FOR RANGE (%) : 96.4
REMARK 3 NUMBER OF REFLECTIONS : 16191
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) : 0.220
REMARK 3 R VALUE (WORKING SET) : 0.218
REMARK 3 FREE R VALUE : 0.270
REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.200
REMARK 3 FREE R VALUE TEST SET COUNT : 892
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) : 2.68
REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.75
REMARK 3 REFLECTION IN BIN (WORKING SET) : 914
REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 73.45
REMARK 3 BIN R VALUE (WORKING SET) : 0.3360
REMARK 3 BIN FREE R VALUE SET COUNT : 60
REMARK 3 BIN FREE R VALUE : 0.3150
REMARK 3
REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT.
REMARK 3 PROTEIN ATOMS : 3521
REMARK 3 NUCLEIC ACID ATOMS : 0
REMARK 3 HETEROGEN ATOMS : 118
REMARK 3 SOLVENT ATOMS : 129
REMARK 3
REMARK 3 B VALUES.
REMARK 3 FROM WILSON PLOT (A**2) : NULL
REMARK 3 MEAN B VALUE (OVERALL, A**2) : 54.02
REMARK 3 OVERALL ANISOTROPIC B VALUE.
REMARK 3 B11 (A**2) : -0.06000
REMARK 3 B22 (A**2) : -1.24000
REMARK 3 B33 (A**2) : 0.82000
REMARK 3 B12 (A**2) : 0.00000
REMARK 3 B13 (A**2) : 0.16000
REMARK 3 B23 (A**2) : 0.00000
REMARK 3
REMARK 3 ESTIMATED OVERALL COORDINATE ERROR.
REMARK 3 ESU BASED ON R VALUE (A): 1.133
REMARK 3 ESU BASED ON FREE R VALUE (A): 0.360
REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.306
REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 27.126
REMARK 3
REMARK 3 CORRELATION COEFFICIENTS.
REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.919
REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.877
REMARK 3
REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT
REMARK 3 BOND LENGTHS REFINED ATOMS (A): 3748 ; 0.010 ; 0.019
REMARK 3 BOND LENGTHS OTHERS (A): 3536 ; 0.002 ; 0.020
REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 5047 ; 1.345 ; 2.002
REMARK 3 BOND ANGLES OTHERS (DEGREES): 8180 ; 0.962 ; 3.003
REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 443 ; 6.624 ; 5.000
REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 174 ;37.207 ;24.368
REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 670 ;16.071 ;15.000
REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 21 ;14.142 ;15.000
REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 530 ; 0.074 ; 0.200
REMARK 3 GENERAL PLANES REFINED ATOMS (A): 4134 ; 0.005 ; 0.021
REMARK 3 GENERAL PLANES OTHERS (A): 837 ; 0.001 ; 0.020
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 : 8
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 -5 A 43
REMARK 3 ORIGIN FOR THE GROUP (A): -39.8324 1.8709 17.6891
REMARK 3 T TENSOR
REMARK 3 T11: 0.4318 T22: 0.1628
REMARK 3 T33: 0.2788 T12: -0.0242
REMARK 3 T13: 0.0084 T23: 0.2103
REMARK 3 L TENSOR
REMARK 3 L11: 3.7186 L22: 1.3193
REMARK 3 L33: 6.4001 L12: -1.8481
REMARK 3 L13: -1.8779 L23: 1.0412
REMARK 3 S TENSOR
REMARK 3 S11: 0.3290 S12: 0.3820 S13: 0.5406
REMARK 3 S21: -0.2798 S22: 0.0358 S23: 0.0108
REMARK 3 S31: -1.5712 S32: -0.1444 S33: -0.3649
REMARK 3
REMARK 3 TLS GROUP : 2
REMARK 3 NUMBER OF COMPONENTS GROUP : 1
REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI
REMARK 3 RESIDUE RANGE : A 44 A 142
REMARK 3 ORIGIN FOR THE GROUP (A): -29.9620 -18.7271 7.7733
REMARK 3 T TENSOR
REMARK 3 T11: 0.1068 T22: 0.1976
REMARK 3 T33: 0.0735 T12: 0.0350
REMARK 3 T13: -0.0073 T23: -0.0764
REMARK 3 L TENSOR
REMARK 3 L11: 5.1591 L22: 2.3413
REMARK 3 L33: 4.6239 L12: 0.4235
REMARK 3 L13: -1.3265 L23: 0.6841
REMARK 3 S TENSOR
REMARK 3 S11: -0.1454 S12: 0.5086 S13: -0.4703
REMARK 3 S21: -0.2634 S22: 0.0843 S23: -0.1446
REMARK 3 S31: 0.1869 S32: 0.1330 S33: 0.0611
REMARK 3
REMARK 3 TLS GROUP : 3
REMARK 3 NUMBER OF COMPONENTS GROUP : 1
REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI
REMARK 3 RESIDUE RANGE : A 143 A 182
REMARK 3 ORIGIN FOR THE GROUP (A): -15.7712 -17.0922 15.1126
REMARK 3 T TENSOR
REMARK 3 T11: 0.0988 T22: 0.5757
REMARK 3 T33: 0.2313 T12: 0.0996
REMARK 3 T13: -0.0173 T23: -0.0212
REMARK 3 L TENSOR
REMARK 3 L11: 4.7339 L22: 7.1349
REMARK 3 L33: 1.6438 L12: -0.6752
REMARK 3 L13: -2.0554 L23: 0.9683
REMARK 3 S TENSOR
REMARK 3 S11: 0.0393 S12: -0.2134 S13: -0.6113
REMARK 3 S21: -0.4108 S22: -0.1193 S23: -0.7611
REMARK 3 S31: 0.0837 S32: 0.6884 S33: 0.0800
REMARK 3
REMARK 3 TLS GROUP : 4
REMARK 3 NUMBER OF COMPONENTS GROUP : 1
REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI
REMARK 3 RESIDUE RANGE : A 183 A 270
REMARK 3 ORIGIN FOR THE GROUP (A): -36.2531 -7.5406 28.3277
REMARK 3 T TENSOR
REMARK 3 T11: 0.1137 T22: 0.0523
REMARK 3 T33: 0.0400 T12: -0.0061
REMARK 3 T13: -0.0290 T23: -0.0373
REMARK 3 L TENSOR
REMARK 3 L11: 3.3118 L22: 1.7356
REMARK 3 L33: 6.1015 L12: -0.5046
REMARK 3 L13: -2.7966 L23: 1.0244
REMARK 3 S TENSOR
REMARK 3 S11: 0.1139 S12: -0.3165 S13: 0.1625
REMARK 3 S21: 0.2141 S22: 0.1136 S23: -0.0998
REMARK 3 S31: -0.3998 S32: 0.4879 S33: -0.2275
REMARK 3
REMARK 3 TLS GROUP : 5
REMARK 3 NUMBER OF COMPONENTS GROUP : 1
REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI
REMARK 3 RESIDUE RANGE : A 271 A 311
REMARK 3 ORIGIN FOR THE GROUP (A): -34.5540 -22.7405 48.0261
REMARK 3 T TENSOR
REMARK 3 T11: 0.7002 T22: 0.8005
REMARK 3 T33: 0.2793 T12: 0.2004
REMARK 3 T13: -0.1174 T23: 0.1325
REMARK 3 L TENSOR
REMARK 3 L11: 1.3455 L22: 6.6129
REMARK 3 L33: 1.9263 L12: 1.6307
REMARK 3 L13: 1.0496 L23: 0.9522
REMARK 3 S TENSOR
REMARK 3 S11: 0.4582 S12: -0.2879 S13: -0.4822
REMARK 3 S21: 0.3305 S22: -0.1107 S23: -0.2233
REMARK 3 S31: 0.4609 S32: 0.5628 S33: -0.3475
REMARK 3
REMARK 3 TLS GROUP : 6
REMARK 3 NUMBER OF COMPONENTS GROUP : 1
REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI
REMARK 3 RESIDUE RANGE : A 312 A 355
REMARK 3 ORIGIN FOR THE GROUP (A): -40.2283 -31.1733 40.2159
REMARK 3 T TENSOR
REMARK 3 T11: 2.0087 T22: 0.2331
REMARK 3 T33: 0.4858 T12: 0.3775
REMARK 3 T13: 0.6648 T23: 0.2060
REMARK 3 L TENSOR
REMARK 3 L11: 2.8657 L22: 3.1112
REMARK 3 L33: 6.2646 L12: 1.1004
REMARK 3 L13: 3.3868 L23: 3.5831
REMARK 3 S TENSOR
REMARK 3 S11: -0.0604 S12: -0.4881 S13: -0.8358
REMARK 3 S21: 1.8553 S22: 0.4412 S23: 0.1040
REMARK 3 S31: 1.9894 S32: -0.0971 S33: -0.3808
REMARK 3
REMARK 3 TLS GROUP : 7
REMARK 3 NUMBER OF COMPONENTS GROUP : 1
REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI
REMARK 3 RESIDUE RANGE : A 356 A 397
REMARK 3 ORIGIN FOR THE GROUP (A): -51.5469 -22.6820 33.8885
REMARK 3 T TENSOR
REMARK 3 T11: 0.3872 T22: 0.2750
REMARK 3 T33: 0.3554 T12: -0.1392
REMARK 3 T13: 0.3228 T23: -0.1106
REMARK 3 L TENSOR
REMARK 3 L11: 2.5006 L22: 3.6017
REMARK 3 L33: 7.6534 L12: -0.0402
REMARK 3 L13: 1.5411 L23: -0.4387
REMARK 3 S TENSOR
REMARK 3 S11: -0.2996 S12: 0.0229 S13: -0.6410
REMARK 3 S21: 0.5857 S22: -0.0023 S23: 0.6171
REMARK 3 S31: 1.0204 S32: -0.9404 S33: 0.3020
REMARK 3
REMARK 3 TLS GROUP : 8
REMARK 3 NUMBER OF COMPONENTS GROUP : 1
REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI
REMARK 3 RESIDUE RANGE : A 398 A 432
REMARK 3 ORIGIN FOR THE GROUP (A): -57.7046 -16.6447 23.2628
REMARK 3 T TENSOR
REMARK 3 T11: 0.2397 T22: 0.8356
REMARK 3 T33: 0.5386 T12: -0.1707
REMARK 3 T13: 0.0478 T23: -0.2808
REMARK 3 L TENSOR
REMARK 3 L11: 2.7812 L22: 8.6468
REMARK 3 L33: 1.4368 L12: 3.0210
REMARK 3 L13: 0.9063 L23: -0.5443
REMARK 3 S TENSOR
REMARK 3 S11: -0.3139 S12: 0.0041 S13: -0.1712
REMARK 3 S21: -0.8046 S22: 0.3637 S23: 1.1188
REMARK 3 S31: 0.2428 S32: -0.8280 S33: -0.0498
REMARK 3
REMARK 3 BULK SOLVENT MODELLING.
REMARK 3 METHOD USED : NULL
REMARK 3 PARAMETERS FOR MASK CALCULATION
REMARK 3 VDW PROBE RADIUS : 1.20
REMARK 3 ION PROBE RADIUS : 0.80
REMARK 3 SHRINKAGE RADIUS : 0.80
REMARK 3
REMARK 3 OTHER REFINEMENT REMARKS: HYDROGENS HAVE BEEN ADDED IN THE RIDING
REMARK 3 POSITIONS U VALUES : WITH TLS ADDED
REMARK 4
REMARK 4 5V3H COMPLIES WITH FORMAT V. 3.30, 13-JUL-11
REMARK 100
REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 10-MAR-17.
REMARK 100 THE DEPOSITION ID IS D_1000226826.
REMARK 200
REMARK 200 EXPERIMENTAL DETAILS
REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION
REMARK 200 DATE OF DATA COLLECTION : 06-SEP-15
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 : SSRF
REMARK 200 BEAMLINE : BL17B1
REMARK 200 X-RAY GENERATOR MODEL : NULL
REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M
REMARK 200 WAVELENGTH OR RANGE (A) : 0.95369
REMARK 200 MONOCHROMATOR : NULL
REMARK 200 OPTICS : NULL
REMARK 200
REMARK 200 DETECTOR TYPE : CCD
REMARK 200 DETECTOR MANUFACTURER : RAYONIX MX300-HS
REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-3000
REMARK 200 DATA SCALING SOFTWARE : HKL-3000
REMARK 200
REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 17477
REMARK 200 RESOLUTION RANGE HIGH (A) : 2.690
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 (%) : 98.8
REMARK 200 DATA REDUNDANCY : 3.700
REMARK 200 R MERGE (I) : NULL
REMARK 200 R SYM (I) : NULL
REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 14.6000
REMARK 200
REMARK 200 IN THE HIGHEST RESOLUTION SHELL.
REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.69
REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.74
REMARK 200 COMPLETENESS FOR SHELL (%) : 100.0
REMARK 200 DATA REDUNDANCY IN SHELL : 3.80
REMARK 200 R MERGE FOR SHELL (I) : 0.58800
REMARK 200 R SYM FOR SHELL (I) : NULL
REMARK 200 <I/SIGMA(I)> FOR SHELL : 2.350
REMARK 200
REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH
REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: NULL
REMARK 200 SOFTWARE USED: NULL
REMARK 200 STARTING MODEL: NULL
REMARK 200
REMARK 200 REMARK: NULL
REMARK 280
REMARK 280 CRYSTAL
REMARK 280 SOLVENT CONTENT, VS (%): 60.52
REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 3.12
REMARK 280
REMARK 280 CRYSTALLIZATION CONDITIONS: 5% V/V ETHANOL, 0.1 M TRIS PH 7.5, 26%
REMARK 280 W/V PEG3350, PH 8.0, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE
REMARK 280 293K
REMARK 290
REMARK 290 CRYSTALLOGRAPHIC SYMMETRY
REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: C 1 2 1
REMARK 290
REMARK 290 SYMOP SYMMETRY
REMARK 290 NNNMMM OPERATOR
REMARK 290 1555 X,Y,Z
REMARK 290 2555 -X,Y,-Z
REMARK 290 3555 X+1/2,Y+1/2,Z
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 0.00000
REMARK 290 SMTRY2 2 0.000000 1.000000 0.000000 0.00000
REMARK 290 SMTRY3 2 0.000000 0.000000 -1.000000 0.00000
REMARK 290 SMTRY1 3 1.000000 0.000000 0.000000 78.78000
REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 27.38750
REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 0.00000
REMARK 290 SMTRY1 4 -1.000000 0.000000 0.000000 78.78000
REMARK 290 SMTRY2 4 0.000000 1.000000 0.000000 27.38750
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 SER A -10
REMARK 465 ILE A -9
REMARK 465 ALA A -8
REMARK 465 ASP A -7
REMARK 465 TYR A -6
REMARK 465 HIS A 433
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 O VAL A 215 O4 PEG A 508 2.18
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 GLN A 70 43.17 -140.02
REMARK 500 LYS A 87 -33.53 -37.43
REMARK 500 ASN A 143 43.35 -81.36
REMARK 500 VAL A 277 53.86 -115.96
REMARK 500 LYS A 281 76.99 -104.84
REMARK 500
REMARK 500 REMARK: NULL
REMARK 500
REMARK 500 GEOMETRY AND STEREOCHEMISTRY
REMARK 500 SUBTOPIC: NON-CIS, NON-TRANS
REMARK 500
REMARK 500 THE FOLLOWING PEPTIDE BONDS DEVIATE SIGNIFICANTLY FROM BOTH
REMARK 500 CIS AND TRANS CONFORMATION. CIS BONDS, IF ANY, ARE LISTED
REMARK 500 ON CISPEP RECORDS. TRANS IS DEFINED AS 180 +/- 30 AND
REMARK 500 CIS IS DEFINED AS 0 +/- 30 DEGREES.
REMARK 500 MODEL OMEGA
REMARK 500 TYR A 311 LYS A 312 -145.31
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 503 ZN
REMARK 620 N RES CSSEQI ATOM
REMARK 620 1 CYS A 52 SG
REMARK 620 2 CYS A 55 SG 109.5
REMARK 620 3 CYS A 74 SG 101.4 96.4
REMARK 620 4 CYS A 78 SG 113.5 117.0 116.8
REMARK 620 N 1 2 3
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 65 SG
REMARK 620 2 CYS A 68 SG 105.8
REMARK 620 3 HIS A 86 NE2 123.6 105.2
REMARK 620 4 CYS A 90 SG 114.5 105.0 101.0
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 209 SG
REMARK 620 2 CYS A 262 SG 114.7
REMARK 620 3 CYS A 264 SG 111.1 104.6
REMARK 620 4 CYS A 267 SG 92.2 116.1 118.1
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 SAM A 501
REMARK 800
REMARK 800 SITE_IDENTIFIER: AC2
REMARK 800 EVIDENCE_CODE: SOFTWARE
REMARK 800 SITE_DESCRIPTION: binding site for residue ZN A 502
REMARK 800
REMARK 800 SITE_IDENTIFIER: AC3
REMARK 800 EVIDENCE_CODE: SOFTWARE
REMARK 800 SITE_DESCRIPTION: binding site for residue ZN A 503
REMARK 800
REMARK 800 SITE_IDENTIFIER: AC4
REMARK 800 EVIDENCE_CODE: SOFTWARE
REMARK 800 SITE_DESCRIPTION: binding site for residue ZN A 504
REMARK 800
REMARK 800 SITE_IDENTIFIER: AC5
REMARK 800 EVIDENCE_CODE: SOFTWARE
REMARK 800 SITE_DESCRIPTION: binding site for residue 8WG A 505
REMARK 800
REMARK 800 SITE_IDENTIFIER: AC6
REMARK 800 EVIDENCE_CODE: SOFTWARE
REMARK 800 SITE_DESCRIPTION: binding site for residue 8WG A 506
REMARK 800
REMARK 800 SITE_IDENTIFIER: AC7
REMARK 800 EVIDENCE_CODE: SOFTWARE
REMARK 800 SITE_DESCRIPTION: binding site for residue PEG A 507
REMARK 800
REMARK 800 SITE_IDENTIFIER: AC8
REMARK 800 EVIDENCE_CODE: SOFTWARE
REMARK 800 SITE_DESCRIPTION: binding site for residue PEG A 508
REMARK 800
REMARK 800 SITE_IDENTIFIER: AC9
REMARK 800 EVIDENCE_CODE: SOFTWARE
REMARK 800 SITE_DESCRIPTION: binding site for residue EDO A 509
REMARK 800
REMARK 800 SITE_IDENTIFIER: AD1
REMARK 800 EVIDENCE_CODE: SOFTWARE
REMARK 800 SITE_DESCRIPTION: binding site for residue GOL A 510
REMARK 800
REMARK 800 SITE_IDENTIFIER: AD2
REMARK 800 EVIDENCE_CODE: SOFTWARE
REMARK 800 SITE_DESCRIPTION: binding site for residue GOL A 511
REMARK 900
REMARK 900 RELATED ENTRIES
REMARK 900 RELATED ID: 5V37 RELATED DB: PDB
DBREF 5V3H A 1 433 UNP Q9NRG4 SMYD2_HUMAN 1 433
SEQADV 5V3H SER A -10 UNP Q9NRG4 EXPRESSION TAG
SEQADV 5V3H ILE A -9 UNP Q9NRG4 EXPRESSION TAG
SEQADV 5V3H ALA A -8 UNP Q9NRG4 EXPRESSION TAG
SEQADV 5V3H ASP A -7 UNP Q9NRG4 EXPRESSION TAG
SEQADV 5V3H TYR A -6 UNP Q9NRG4 EXPRESSION TAG
SEQADV 5V3H LYS A -5 UNP Q9NRG4 EXPRESSION TAG
SEQADV 5V3H ASP A -4 UNP Q9NRG4 EXPRESSION TAG
SEQADV 5V3H ASP A -3 UNP Q9NRG4 EXPRESSION TAG
SEQADV 5V3H ASP A -2 UNP Q9NRG4 EXPRESSION TAG
SEQADV 5V3H ASP A -1 UNP Q9NRG4 EXPRESSION TAG
SEQADV 5V3H LYS A 0 UNP Q9NRG4 EXPRESSION TAG
SEQRES 1 A 444 SER ILE ALA ASP TYR LYS ASP ASP ASP ASP LYS MET ARG
SEQRES 2 A 444 ALA GLU GLY LEU GLY GLY LEU GLU ARG PHE CYS SER PRO
SEQRES 3 A 444 GLY LYS GLY ARG GLY LEU ARG ALA LEU GLN PRO PHE GLN
SEQRES 4 A 444 VAL GLY ASP LEU LEU PHE SER CYS PRO ALA TYR ALA TYR
SEQRES 5 A 444 VAL LEU THR VAL ASN GLU ARG GLY ASN HIS CYS GLU TYR
SEQRES 6 A 444 CYS PHE THR ARG LYS GLU GLY LEU SER LYS CYS GLY ARG
SEQRES 7 A 444 CYS LYS GLN ALA PHE TYR CYS ASN VAL GLU CYS GLN LYS
SEQRES 8 A 444 GLU ASP TRP PRO MET HIS LYS LEU GLU CYS SER PRO MET
SEQRES 9 A 444 VAL VAL PHE GLY GLU ASN TRP ASN PRO SER GLU THR VAL
SEQRES 10 A 444 ARG LEU THR ALA ARG ILE LEU ALA LYS GLN LYS ILE HIS
SEQRES 11 A 444 PRO GLU ARG THR PRO SER GLU LYS LEU LEU ALA VAL LYS
SEQRES 12 A 444 GLU PHE GLU SER HIS LEU ASP LYS LEU ASP ASN GLU LYS
SEQRES 13 A 444 LYS ASP LEU ILE GLN SER ASP ILE ALA ALA LEU HIS HIS
SEQRES 14 A 444 PHE TYR SER LYS HIS LEU GLY PHE PRO ASP ASN ASP SER
SEQRES 15 A 444 LEU VAL VAL LEU PHE ALA GLN VAL ASN CYS ASN GLY PHE
SEQRES 16 A 444 THR ILE GLU ASP GLU GLU LEU SER HIS LEU GLY SER ALA
SEQRES 17 A 444 ILE PHE PRO ASP VAL ALA LEU MET ASN HIS SER CYS CYS
SEQRES 18 A 444 PRO ASN VAL ILE VAL THR TYR LYS GLY THR LEU ALA GLU
SEQRES 19 A 444 VAL ARG ALA VAL GLN GLU ILE LYS PRO GLY GLU GLU VAL
SEQRES 20 A 444 PHE THR SER TYR ILE ASP LEU LEU TYR PRO THR GLU ASP
SEQRES 21 A 444 ARG ASN ASP ARG LEU ARG ASP SER TYR PHE PHE THR CYS
SEQRES 22 A 444 GLU CYS GLN GLU CYS THR THR LYS ASP LYS ASP LYS ALA
SEQRES 23 A 444 LYS VAL GLU ILE ARG LYS LEU SER ASP PRO PRO LYS ALA
SEQRES 24 A 444 GLU ALA ILE ARG ASP MET VAL ARG TYR ALA ARG ASN VAL
SEQRES 25 A 444 ILE GLU GLU PHE ARG ARG ALA LYS HIS TYR LYS SER PRO
SEQRES 26 A 444 SER GLU LEU LEU GLU ILE CYS GLU LEU SER GLN GLU LYS
SEQRES 27 A 444 MET SER SER VAL PHE GLU ASP SER ASN VAL TYR MET LEU
SEQRES 28 A 444 HIS MET MET TYR GLN ALA MET GLY VAL CYS LEU TYR MET
SEQRES 29 A 444 GLN ASP TRP GLU GLY ALA LEU GLN TYR GLY GLN LYS ILE
SEQRES 30 A 444 ILE LYS PRO TYR SER LYS HIS TYR PRO LEU TYR SER LEU
SEQRES 31 A 444 ASN VAL ALA SER MET TRP LEU LYS LEU GLY ARG LEU TYR
SEQRES 32 A 444 MET GLY LEU GLU HIS LYS ALA ALA GLY GLU LYS ALA LEU
SEQRES 33 A 444 LYS LYS ALA ILE ALA ILE MET GLU VAL ALA HIS GLY LYS
SEQRES 34 A 444 ASP HIS PRO TYR ILE SER GLU ILE LYS GLN GLU ILE GLU
SEQRES 35 A 444 SER HIS
HET SAM A 501 27
HET ZN A 502 1
HET ZN A 503 1
HET ZN A 504 1
HET 8WG A 505 29
HET 8WG A 506 29
HET PEG A 507 7
HET PEG A 508 7
HET EDO A 509 4
HET GOL A 510 6
HET GOL A 511 6
HETNAM SAM S-ADENOSYLMETHIONINE
HETNAM ZN ZINC ION
HETNAM 8WG N-[1-({1-[(4-CHLOROPHENYL)METHYL]-1H-PYRAZOL-4-
HETNAM 2 8WG YL}METHYL)AZETIDIN-3-YL]-1-CYCLOPROPYL-1H-1,2,3-
HETNAM 3 8WG TRIAZOLE-4-CARBOXAMIDE
HETNAM PEG DI(HYDROXYETHYL)ETHER
HETNAM EDO 1,2-ETHANEDIOL
HETNAM GOL GLYCEROL
HETSYN EDO ETHYLENE GLYCOL
HETSYN GOL GLYCERIN; PROPANE-1,2,3-TRIOL
FORMUL 2 SAM C15 H22 N6 O5 S
FORMUL 3 ZN 3(ZN 2+)
FORMUL 6 8WG 2(C20 H22 CL N7 O)
FORMUL 8 PEG 2(C4 H10 O3)
FORMUL 10 EDO C2 H6 O2
FORMUL 11 GOL 2(C3 H8 O3)
FORMUL 13 HOH *129(H2 O)
HELIX 1 AA1 LYS A -5 GLY A 5 1 11
HELIX 2 AA2 VAL A 45 ARG A 48 5 4
HELIX 3 AA3 ASN A 75 ASP A 82 1 8
HELIX 4 AA4 ASP A 82 LYS A 87 1 6
HELIX 5 AA5 GLU A 89 GLY A 97 1 9
HELIX 6 AA6 SER A 103 HIS A 119 1 17
HELIX 7 AA7 THR A 123 LYS A 127 5 5
HELIX 8 AA8 ALA A 130 PHE A 134 5 5
HELIX 9 AA9 HIS A 137 LEU A 141 5 5
HELIX 10 AB1 GLU A 144 SER A 161 1 18
HELIX 11 AB2 ASP A 168 GLY A 183 1 16
HELIX 12 AB3 ASP A 201 MET A 205 5 5
HELIX 13 AB4 PRO A 246 PHE A 259 1 14
HELIX 14 AB5 CYS A 264 LYS A 270 1 7
HELIX 15 AB6 LYS A 272 VAL A 277 1 6
HELIX 16 AB7 LYS A 287 LYS A 312 1 26
HELIX 17 AB8 SER A 313 SER A 329 1 17
HELIX 18 AB9 ASN A 336 MET A 353 1 18
HELIX 19 AC1 ASP A 355 TYR A 374 1 20
HELIX 20 AC2 SER A 378 LEU A 395 1 18
HELIX 21 AC3 HIS A 397 HIS A 416 1 20
HELIX 22 AC4 HIS A 420 GLU A 431 1 12
SHEET 1 AA1 2 LEU A 9 CYS A 13 0
SHEET 2 AA1 2 ARG A 19 ALA A 23 -1 O GLY A 20 N PHE A 12
SHEET 1 AA2 3 LEU A 32 PRO A 37 0
SHEET 2 AA2 3 LEU A 221 ALA A 226 -1 O VAL A 224 N LEU A 33
SHEET 3 AA2 3 VAL A 213 LYS A 218 -1 N LYS A 218 O LEU A 221
SHEET 1 AA3 3 ALA A 40 LEU A 43 0
SHEET 2 AA3 3 HIS A 193 ILE A 198 -1 O ILE A 198 N ALA A 40
SHEET 3 AA3 3 PHE A 184 GLU A 187 -1 N ILE A 186 O LEU A 194
SHEET 1 AA4 2 SER A 63 LYS A 64 0
SHEET 2 AA4 2 PHE A 72 TYR A 73 -1 O TYR A 73 N SER A 63
SHEET 1 AA5 2 ASN A 206 HIS A 207 0
SHEET 2 AA5 2 PHE A 237 THR A 238 1 O THR A 238 N ASN A 206
LINK SG CYS A 52 ZN ZN A 503 1555 1555 2.34
LINK SG CYS A 55 ZN ZN A 503 1555 1555 2.38
LINK SG CYS A 65 ZN ZN A 504 1555 1555 2.35
LINK SG CYS A 68 ZN ZN A 504 1555 1555 2.34
LINK SG CYS A 74 ZN ZN A 503 1555 1555 2.34
LINK SG CYS A 78 ZN ZN A 503 1555 1555 2.35
LINK NE2 HIS A 86 ZN ZN A 504 1555 1555 2.18
LINK SG CYS A 90 ZN ZN A 504 1555 1555 2.35
LINK SG CYS A 209 ZN ZN A 502 1555 1555 2.35
LINK SG CYS A 262 ZN ZN A 502 1555 1555 2.33
LINK SG CYS A 264 ZN ZN A 502 1555 1555 2.35
LINK SG CYS A 267 ZN ZN A 502 1555 1555 2.33
SITE 1 AC1 14 LYS A 17 ARG A 19 GLU A 135 HIS A 137
SITE 2 AC1 14 CYS A 181 ASN A 182 ALA A 203 LEU A 204
SITE 3 AC1 14 ASN A 206 HIS A 207 TYR A 240 TYR A 258
SITE 4 AC1 14 PHE A 260 HOH A 622
SITE 1 AC2 4 CYS A 209 CYS A 262 CYS A 264 CYS A 267
SITE 1 AC3 4 CYS A 52 CYS A 55 CYS A 74 CYS A 78
SITE 1 AC4 4 CYS A 65 CYS A 68 HIS A 86 CYS A 90
SITE 1 AC5 15 GLY A 183 PHE A 184 THR A 185 GLU A 187
SITE 2 AC5 15 ASP A 188 GLU A 189 VAL A 215 TYR A 217
SITE 3 AC5 15 TYR A 240 TYR A 258 LEU A 379 HIS A 416
SITE 4 AC5 15 8WG A 506 PEG A 508 GOL A 511
SITE 1 AC6 11 LEU A 108 GLY A 183 PHE A 184 THR A 185
SITE 2 AC6 11 SER A 196 ILE A 241 ASP A 242 TYR A 245
SITE 3 AC6 11 ARG A 253 HIS A 341 8WG A 505
SITE 1 AC7 7 PRO A 211 VAL A 213 VAL A 215 THR A 238
SITE 2 AC7 7 SER A 239 PEG A 508 GOL A 511
SITE 1 AC8 8 ILE A 214 VAL A 215 SER A 378 LEU A 379
SITE 2 AC8 8 ASN A 380 8WG A 505 PEG A 507 GOL A 511
SITE 1 AC9 5 ALA A 38 TYR A 39 LYS A 115 HOH A 636
SITE 2 AC9 5 HOH A 652
SITE 1 AD1 1 GLU A 104
SITE 1 AD2 7 SER A 239 TYR A 240 ILE A 241 ASP A 242
SITE 2 AD2 7 8WG A 505 PEG A 507 PEG A 508
CRYST1 157.560 54.775 79.702 90.00 114.22 90.00 C 1 2 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 0.006347 0.000000 0.002855 0.00000
SCALE2 0.000000 0.018257 0.000000 0.00000
SCALE3 0.000000 0.000000 0.013757 0.00000