HEADER DNA BINDING PROTEIN/DNA 03-APR-09 3GYH
TITLE CRYSTAL STRUCTURE ANALYSIS OF S. POMBE ATL IN COMPLEX WITH DAMAGED DNA
TITLE 2 CONTAINING POB
COMPND MOL_ID: 1;
COMPND 2 MOLECULE: ALKYLTRANSFERASE-LIKE PROTEIN 1;
COMPND 3 CHAIN: X;
COMPND 4 ENGINEERED: YES;
COMPND 5 MOL_ID: 2;
COMPND 6 MOLECULE: DNA (5'-D(*GP*CP*CP*AP*TP*GP*GP*CP*TP*AP*GP*TP*A)-3');
COMPND 7 CHAIN: Y;
COMPND 8 ENGINEERED: YES;
COMPND 9 MOL_ID: 3;
COMPND 10 MOLECULE: DNA (5'-D(*CP*TP*AP*CP*TP*AP*GP*CP*CP*AP*TP*GP*G)-3');
COMPND 11 CHAIN: Z;
COMPND 12 ENGINEERED: YES
SOURCE MOL_ID: 1;
SOURCE 2 ORGANISM_SCIENTIFIC: SCHIZOSACCHAROMYCES POMBE;
SOURCE 3 ORGANISM_COMMON: FISSION YEAST;
SOURCE 4 ORGANISM_TAXID: 4896;
SOURCE 5 GENE: ATL1, SPAC1250.04C;
SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI;
SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562;
SOURCE 8 MOL_ID: 2;
SOURCE 9 SYNTHETIC: YES;
SOURCE 10 MOL_ID: 3;
SOURCE 11 SYNTHETIC: YES
KEYWDS DNA DAMAGE, DNA REPAIR, DNA-BINDING, DNA BINDING PROTEIN-DNA COMPLEX
EXPDTA X-RAY DIFFRACTION
AUTHOR J.L.TUBBS,A.S.ARVAI,J.A.TAINER,D.S.SHIN
REVDAT 4 21-FEB-24 3GYH 1 REMARK SEQADV LINK
REVDAT 3 13-JUL-11 3GYH 1 VERSN
REVDAT 2 28-JUL-09 3GYH 1 JRNL
REVDAT 1 16-JUN-09 3GYH 0
JRNL AUTH J.L.TUBBS,V.LATYPOV,S.KANUGULA,A.BUTT,M.MELIKISHVILI,
JRNL AUTH 2 R.KRAEHENBUEHL,O.FLECK,A.MARRIOTT,A.J.WATSON,B.VERBEEK,
JRNL AUTH 3 G.MCGOWN,M.THORNCROFT,M.F.SANTIBANEZ-KOREF,C.MILLINGTON,
JRNL AUTH 4 A.S.ARVAI,M.D.KROEGER,L.A.PETERSON,D.M.WILLIAMS,M.G.FRIED,
JRNL AUTH 5 G.P.MARGISON,A.E.PEGG,J.A.TAINER
JRNL TITL FLIPPING OF ALKYLATED DNA DAMAGE BRIDGES BASE AND NUCLEOTIDE
JRNL TITL 2 EXCISION REPAIR.
JRNL REF NATURE V. 459 808 2009
JRNL REFN ISSN 0028-0836
JRNL PMID 19516334
JRNL DOI 10.1038/NATURE08076
REMARK 2
REMARK 2 RESOLUTION. 2.80 ANGSTROMS.
REMARK 3
REMARK 3 REFINEMENT.
REMARK 3 PROGRAM : REFMAC 5.2.0019
REMARK 3 AUTHORS : MURSHUDOV,SKUBAK,LEBEDEV,PANNU,STEINER,
REMARK 3 : NICHOLLS,WINN,LONG,VAGIN
REMARK 3
REMARK 3 REFINEMENT TARGET : MAXIMUM LIKELIHOOD
REMARK 3
REMARK 3 DATA USED IN REFINEMENT.
REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.80
REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 34.94
REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000
REMARK 3 COMPLETENESS FOR RANGE (%) : 93.9
REMARK 3 NUMBER OF REFLECTIONS : 6078
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) : 0.243
REMARK 3 R VALUE (WORKING SET) : 0.240
REMARK 3 FREE R VALUE : 0.285
REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.600
REMARK 3 FREE R VALUE TEST SET COUNT : 341
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) : 2.80
REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.87
REMARK 3 REFLECTION IN BIN (WORKING SET) : 225
REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 73.10
REMARK 3 BIN R VALUE (WORKING SET) : 0.4450
REMARK 3 BIN FREE R VALUE SET COUNT : 6
REMARK 3 BIN FREE R VALUE : 0.6380
REMARK 3
REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT.
REMARK 3 PROTEIN ATOMS : 890
REMARK 3 NUCLEIC ACID ATOMS : 527
REMARK 3 HETEROGEN ATOMS : 11
REMARK 3 SOLVENT ATOMS : 2
REMARK 3
REMARK 3 B VALUES.
REMARK 3 B VALUE TYPE : LIKELY RESIDUAL
REMARK 3 FROM WILSON PLOT (A**2) : NULL
REMARK 3 MEAN B VALUE (OVERALL, A**2) : 84.27
REMARK 3 OVERALL ANISOTROPIC B VALUE.
REMARK 3 B11 (A**2) : 5.59000
REMARK 3 B22 (A**2) : 5.59000
REMARK 3 B33 (A**2) : -8.38000
REMARK 3 B12 (A**2) : 2.79000
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): 6.232
REMARK 3 ESU BASED ON FREE R VALUE (A): 0.414
REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.352
REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 42.393
REMARK 3
REMARK 3 CORRELATION COEFFICIENTS.
REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.935
REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.903
REMARK 3
REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT
REMARK 3 BOND LENGTHS REFINED ATOMS (A): 1515 ; 0.008 ; 0.021
REMARK 3 BOND LENGTHS OTHERS (A): NULL ; NULL ; NULL
REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 2146 ; 1.308 ; 2.398
REMARK 3 BOND ANGLES OTHERS (DEGREES): NULL ; NULL ; NULL
REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 107 ; 9.552 ; 5.000
REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 46 ;39.370 ;23.043
REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 163 ;24.108 ;15.000
REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 8 ;22.091 ;15.000
REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 225 ; 0.082 ; 0.200
REMARK 3 GENERAL PLANES REFINED ATOMS (A): 987 ; 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): 537 ; 1.000 ; 1.500
REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL
REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 869 ; 1.951 ; 2.000
REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL
REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 978 ; 2.840 ; 3.000
REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL
REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 1277 ; 4.494 ; 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 : 3
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 : X 1 X 108
REMARK 3 ORIGIN FOR THE GROUP (A): 28.7896 -21.3040 1.8135
REMARK 3 T TENSOR
REMARK 3 T11: 0.1113 T22: 0.2578
REMARK 3 T33: 0.2130 T12: 0.0865
REMARK 3 T13: 0.0618 T23: 0.0360
REMARK 3 L TENSOR
REMARK 3 L11: 2.0731 L22: 1.4976
REMARK 3 L33: 4.4228 L12: -1.0662
REMARK 3 L13: 0.3162 L23: -0.7987
REMARK 3 S TENSOR
REMARK 3 S11: -0.0770 S12: 0.2720 S13: 0.0127
REMARK 3 S21: 0.0728 S22: 0.0276 S23: -0.0510
REMARK 3 S31: -0.4299 S32: -0.1499 S33: 0.0493
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 : Y 201 Y 213
REMARK 3 ORIGIN FOR THE GROUP (A): 29.7547 -38.3685 6.7585
REMARK 3 T TENSOR
REMARK 3 T11: 0.2658 T22: 0.2788
REMARK 3 T33: 0.2015 T12: -0.0357
REMARK 3 T13: 0.1401 T23: -0.0390
REMARK 3 L TENSOR
REMARK 3 L11: 1.3533 L22: 3.5641
REMARK 3 L33: 6.1664 L12: 0.7280
REMARK 3 L13: 1.1953 L23: 1.5781
REMARK 3 S TENSOR
REMARK 3 S11: -0.3327 S12: 0.0133 S13: 0.0125
REMARK 3 S21: -0.1573 S22: 0.2228 S23: -0.0374
REMARK 3 S31: 0.4091 S32: -0.2994 S33: 0.1099
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 : Z 214 Z 226
REMARK 3 ORIGIN FOR THE GROUP (A): 29.8901 -38.9211 6.0434
REMARK 3 T TENSOR
REMARK 3 T11: 0.1132 T22: 0.1479
REMARK 3 T33: 0.1272 T12: 0.0223
REMARK 3 T13: 0.0379 T23: 0.0278
REMARK 3 L TENSOR
REMARK 3 L11: 1.3445 L22: 1.5510
REMARK 3 L33: 10.1397 L12: 0.1743
REMARK 3 L13: -1.9671 L23: 0.4917
REMARK 3 S TENSOR
REMARK 3 S11: 0.0126 S12: 0.2219 S13: 0.2456
REMARK 3 S21: 0.0988 S22: -0.0488 S23: -0.1716
REMARK 3 S31: 0.6378 S32: -0.6942 S33: 0.0362
REMARK 3
REMARK 3 BULK SOLVENT MODELLING.
REMARK 3 METHOD USED : MASK
REMARK 3 PARAMETERS FOR MASK CALCULATION
REMARK 3 VDW PROBE RADIUS : 1.40
REMARK 3 ION PROBE RADIUS : 0.80
REMARK 3 SHRINKAGE RADIUS : 0.80
REMARK 3
REMARK 3 OTHER REFINEMENT REMARKS: HYDROGENS HAVE BEEN ADDED IN THE RIDING
REMARK 3 POSITIONS U VALUES: RESIDUAL ONLY
REMARK 4
REMARK 4 3GYH COMPLIES WITH FORMAT V. 3.30, 13-JUL-11
REMARK 100
REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 28-MAY-09.
REMARK 100 THE DEPOSITION ID IS D_1000052464.
REMARK 200
REMARK 200 EXPERIMENTAL DETAILS
REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION
REMARK 200 DATE OF DATA COLLECTION : 30-MAY-08
REMARK 200 TEMPERATURE (KELVIN) : NULL
REMARK 200 PH : NULL
REMARK 200 NUMBER OF CRYSTALS USED : 1
REMARK 200
REMARK 200 SYNCHROTRON (Y/N) : Y
REMARK 200 RADIATION SOURCE : SSRL
REMARK 200 BEAMLINE : BL11-1
REMARK 200 X-RAY GENERATOR MODEL : NULL
REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M
REMARK 200 WAVELENGTH OR RANGE (A) : NULL
REMARK 200 MONOCHROMATOR : NULL
REMARK 200 OPTICS : NULL
REMARK 200
REMARK 200 DETECTOR TYPE : NULL
REMARK 200 DETECTOR MANUFACTURER : NULL
REMARK 200 INTENSITY-INTEGRATION SOFTWARE : NULL
REMARK 200 DATA SCALING SOFTWARE : NULL
REMARK 200
REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 6078
REMARK 200 RESOLUTION RANGE HIGH (A) : 2.800
REMARK 200 RESOLUTION RANGE LOW (A) : 35.000
REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL
REMARK 200
REMARK 200 OVERALL.
REMARK 200 COMPLETENESS FOR RANGE (%) : NULL
REMARK 200 DATA REDUNDANCY : NULL
REMARK 200 R MERGE (I) : NULL
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) : NULL
REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : NULL
REMARK 200 COMPLETENESS FOR SHELL (%) : NULL
REMARK 200 DATA REDUNDANCY IN SHELL : NULL
REMARK 200 R MERGE FOR SHELL (I) : NULL
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: 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 (%): 56.83
REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.85
REMARK 280
REMARK 280 CRYSTALLIZATION CONDITIONS: NULL
REMARK 290
REMARK 290 CRYSTALLOGRAPHIC SYMMETRY
REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 61 2 2
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 7555 Y,X,-Z+1/3
REMARK 290 8555 X-Y,-Y,-Z
REMARK 290 9555 -X,-X+Y,-Z+2/3
REMARK 290 10555 -Y,-X,-Z+5/6
REMARK 290 11555 -X+Y,Y,-Z+1/2
REMARK 290 12555 X,X-Y,-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 78.51533
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 157.03067
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 117.77300
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 196.28833
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 39.25767
REMARK 290 SMTRY1 7 -0.500000 0.866025 0.000000 0.00000
REMARK 290 SMTRY2 7 0.866025 0.500000 0.000000 0.00000
REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 78.51533
REMARK 290 SMTRY1 8 1.000000 0.000000 0.000000 0.00000
REMARK 290 SMTRY2 8 0.000000 -1.000000 0.000000 0.00000
REMARK 290 SMTRY3 8 0.000000 0.000000 -1.000000 0.00000
REMARK 290 SMTRY1 9 -0.500000 -0.866025 0.000000 0.00000
REMARK 290 SMTRY2 9 -0.866025 0.500000 0.000000 0.00000
REMARK 290 SMTRY3 9 0.000000 0.000000 -1.000000 157.03067
REMARK 290 SMTRY1 10 0.500000 -0.866025 0.000000 0.00000
REMARK 290 SMTRY2 10 -0.866025 -0.500000 0.000000 0.00000
REMARK 290 SMTRY3 10 0.000000 0.000000 -1.000000 196.28833
REMARK 290 SMTRY1 11 -1.000000 0.000000 0.000000 0.00000
REMARK 290 SMTRY2 11 0.000000 1.000000 0.000000 0.00000
REMARK 290 SMTRY3 11 0.000000 0.000000 -1.000000 117.77300
REMARK 290 SMTRY1 12 0.500000 0.866025 0.000000 0.00000
REMARK 290 SMTRY2 12 0.866025 -0.500000 0.000000 0.00000
REMARK 290 SMTRY3 12 0.000000 0.000000 -1.000000 39.25767
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: TRIMERIC
REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: TRIMERIC
REMARK 350 SOFTWARE USED: PISA
REMARK 350 TOTAL BURIED SURFACE AREA: 3530 ANGSTROM**2
REMARK 350 SURFACE AREA OF THE COMPLEX: 9650 ANGSTROM**2
REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -15.0 KCAL/MOL
REMARK 350 APPLY THE FOLLOWING TO CHAINS: X, Y, Z
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 X 109
REMARK 465 SER X 110
REMARK 465 HIS X 111
REMARK 465 HIS X 112
REMARK 465 HIS X 113
REMARK 465 HIS X 114
REMARK 465 HIS X 115
REMARK 465 HIS X 116
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 NH2 ARG X 39 N3 DC Z 221 2.17
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 NH2 ARG X 2 OD2 ASP X 12 12545 2.11
REMARK 500
REMARK 500 REMARK: NULL
REMARK 500
REMARK 500 GEOMETRY AND STEREOCHEMISTRY
REMARK 500 SUBTOPIC: COVALENT BOND LENGTHS
REMARK 500
REMARK 500 THE STEREOCHEMICAL PARAMETERS OF THE FOLLOWING RESIDUES
REMARK 500 HAVE VALUES WHICH DEVIATE FROM EXPECTED VALUES BY MORE
REMARK 500 THAN 6*RMSD (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN
REMARK 500 IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE).
REMARK 500
REMARK 500 STANDARD TABLE:
REMARK 500 FORMAT: (10X,I3,1X,2(A3,1X,A1,I4,A1,1X,A4,3X),1X,F6.3)
REMARK 500
REMARK 500 EXPECTED VALUES PROTEIN: ENGH AND HUBER, 1999
REMARK 500 EXPECTED VALUES NUCLEIC ACID: CLOWNEY ET AL 1996
REMARK 500
REMARK 500 M RES CSSEQI ATM1 RES CSSEQI ATM2 DEVIATION
REMARK 500 DG Y 207 C6 DG Y 207 N1 -0.045
REMARK 500 DG Y 207 C5 DG Y 207 N7 -0.038
REMARK 500 DG Y 207 N7 DG Y 207 C8 0.055
REMARK 500 DG Y 207 C6 DG Y 207 O6 0.135
REMARK 500
REMARK 500 REMARK: NULL
REMARK 500
REMARK 500 GEOMETRY AND STEREOCHEMISTRY
REMARK 500 SUBTOPIC: COVALENT BOND ANGLES
REMARK 500
REMARK 500 THE STEREOCHEMICAL PARAMETERS OF THE FOLLOWING RESIDUES
REMARK 500 HAVE VALUES WHICH DEVIATE FROM EXPECTED VALUES BY MORE
REMARK 500 THAN 6*RMSD (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN
REMARK 500 IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE).
REMARK 500
REMARK 500 STANDARD TABLE:
REMARK 500 FORMAT: (10X,I3,1X,A3,1X,A1,I4,A1,3(1X,A4,2X),12X,F5.1)
REMARK 500
REMARK 500 EXPECTED VALUES PROTEIN: ENGH AND HUBER, 1999
REMARK 500 EXPECTED VALUES NUCLEIC ACID: CLOWNEY ET AL 1996
REMARK 500
REMARK 500 M RES CSSEQI ATM1 ATM2 ATM3
REMARK 500 DT Y 205 O4' - C1' - N1 ANGL. DEV. = -4.2 DEGREES
REMARK 500 DG Y 206 C3' - O3' - P ANGL. DEV. = -8.3 DEGREES
REMARK 500 DG Y 207 O3' - P - OP2 ANGL. DEV. = 28.6 DEGREES
REMARK 500 DG Y 207 O3' - P - OP1 ANGL. DEV. = -27.4 DEGREES
REMARK 500 DG Y 207 O4' - C1' - N9 ANGL. DEV. = 2.3 DEGREES
REMARK 500 DG Y 207 C6 - N1 - C2 ANGL. DEV. = -4.9 DEGREES
REMARK 500 DG Y 207 C2 - N3 - C4 ANGL. DEV. = 7.8 DEGREES
REMARK 500 DG Y 207 N3 - C4 - C5 ANGL. DEV. = -9.2 DEGREES
REMARK 500 DG Y 207 C5 - C6 - N1 ANGL. DEV. = 7.1 DEGREES
REMARK 500 DG Y 207 C4 - C5 - N7 ANGL. DEV. = -4.3 DEGREES
REMARK 500 DG Y 207 C5 - N7 - C8 ANGL. DEV. = 3.6 DEGREES
REMARK 500 DG Y 207 N7 - C8 - N9 ANGL. DEV. = -4.5 DEGREES
REMARK 500 DG Y 207 N9 - C4 - C5 ANGL. DEV. = 2.9 DEGREES
REMARK 500 DG Y 207 N3 - C4 - N9 ANGL. DEV. = 6.3 DEGREES
REMARK 500 DG Y 207 C5 - C6 - O6 ANGL. DEV. = -8.2 DEGREES
REMARK 500 DG Y 207 C3' - O3' - P ANGL. DEV. = -12.8 DEGREES
REMARK 500 DC Y 208 O3' - P - OP2 ANGL. DEV. = 16.1 DEGREES
REMARK 500 DC Y 208 O3' - P - OP1 ANGL. DEV. = -15.9 DEGREES
REMARK 500 DG Y 211 O4' - C1' - N9 ANGL. DEV. = 3.9 DEGREES
REMARK 500 DC Z 214 O4' - C1' - N1 ANGL. DEV. = 2.5 DEGREES
REMARK 500 DT Z 218 O4' - C1' - N1 ANGL. DEV. = 4.3 DEGREES
REMARK 500 DT Z 224 N3 - C4 - O4 ANGL. DEV. = 4.1 DEGREES
REMARK 500 DG Z 225 O4' - C1' - N9 ANGL. DEV. = 2.8 DEGREES
REMARK 500 DG Z 226 O4' - C4' - C3' ANGL. DEV. = -2.8 DEGREES
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 TYR X 25 -64.48 -29.69
REMARK 500 HIS X 47 36.11 -98.31
REMARK 500 HIS X 53 47.22 -104.84
REMARK 500 ILE X 60 -163.58 -103.02
REMARK 500 ILE X 71 46.72 -96.23
REMARK 500 SER X 72 163.35 40.39
REMARK 500 THR X 92 -144.18 -104.27
REMARK 500 LEU X 94 52.47 -140.22
REMARK 500 GLU X 96 76.52 -7.11
REMARK 500 TYR X 97 129.23 -38.59
REMARK 500 GLU X 103 -82.14 -54.45
REMARK 500 LYS X 107 85.65 -156.40
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 SER X 93 LEU X 94 123.74
REMARK 500
REMARK 500 REMARK: NULL
REMARK 800
REMARK 800 SITE
REMARK 800 SITE_IDENTIFIER: AC1
REMARK 800 EVIDENCE_CODE: SOFTWARE
REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE PBO Y 200
REMARK 900
REMARK 900 RELATED ENTRIES
REMARK 900 RELATED ID: 3GVA RELATED DB: PDB
REMARK 900 SAME PROTEIN WITHOUT DNA
REMARK 900 RELATED ID: 3GX4 RELATED DB: PDB
REMARK 900 SAME PROTEIN WITH DNA
DBREF 3GYH X 1 108 UNP Q9UTN9 ATL1_SCHPO 1 108
DBREF 3GYH Y 201 213 PDB 3GYH 3GYH 201 213
DBREF 3GYH Z 214 226 PDB 3GYH 3GYH 214 226
SEQADV 3GYH GLY X 109 UNP Q9UTN9 EXPRESSION TAG
SEQADV 3GYH SER X 110 UNP Q9UTN9 EXPRESSION TAG
SEQADV 3GYH HIS X 111 UNP Q9UTN9 EXPRESSION TAG
SEQADV 3GYH HIS X 112 UNP Q9UTN9 EXPRESSION TAG
SEQADV 3GYH HIS X 113 UNP Q9UTN9 EXPRESSION TAG
SEQADV 3GYH HIS X 114 UNP Q9UTN9 EXPRESSION TAG
SEQADV 3GYH HIS X 115 UNP Q9UTN9 EXPRESSION TAG
SEQADV 3GYH HIS X 116 UNP Q9UTN9 EXPRESSION TAG
SEQRES 1 X 116 MET ARG MET ASP GLU PHE TYR THR LYS VAL TYR ASP ALA
SEQRES 2 X 116 VAL CYS GLU ILE PRO TYR GLY LYS VAL SER THR TYR GLY
SEQRES 3 X 116 GLU ILE ALA ARG TYR VAL GLY MET PRO SER TYR ALA ARG
SEQRES 4 X 116 GLN VAL GLY GLN ALA MET LYS HIS LEU HIS PRO GLU THR
SEQRES 5 X 116 HIS VAL PRO TRP HIS ARG VAL ILE ASN SER ARG GLY THR
SEQRES 6 X 116 ILE SER LYS ARG ASP ILE SER ALA GLY GLU GLN ARG GLN
SEQRES 7 X 116 LYS ASP ARG LEU GLU GLU GLU GLY VAL GLU ILE TYR GLN
SEQRES 8 X 116 THR SER LEU GLY GLU TYR LYS LEU ASN LEU PRO GLU TYR
SEQRES 9 X 116 MET TRP LYS PRO GLY SER HIS HIS HIS HIS HIS HIS
SEQRES 1 Y 13 DG DC DC DA DT DG DG DC DT DA DG DT DA
SEQRES 1 Z 13 DC DT DA DC DT DA DG DC DC DA DT DG DG
HET PBO Y 200 11
HETNAM PBO 1-PYRIDIN-3-YLBUTAN-1-ONE
FORMUL 4 PBO C9 H11 N O
FORMUL 5 HOH *2(H2 O)
HELIX 1 1 ARG X 2 CYS X 15 1 14
HELIX 2 2 TYR X 25 VAL X 32 1 8
HELIX 3 3 TYR X 37 HIS X 47 1 11
HELIX 4 4 PRO X 55 HIS X 57 5 3
HELIX 5 5 SER X 72 GLY X 74 5 3
HELIX 6 6 GLU X 75 GLY X 86 1 12
SHEET 1 A 2 SER X 23 THR X 24 0
SHEET 2 A 2 VAL X 59 ILE X 60 1 O ILE X 60 N SER X 23
LINK C10 PBO Y 200 O6 DG Y 207 1555 1555 1.43
SITE 1 AC1 8 MET X 45 LEU X 48 PRO X 50 TRP X 56
SITE 2 AC1 8 ARG X 77 ARG X 81 DG Y 207 DG Y 211
CRYST1 60.180 60.180 235.546 90.00 90.00 120.00 P 61 2 2 12
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 0.016617 0.009594 0.000000 0.00000
SCALE2 0.000000 0.019187 0.000000 0.00000
SCALE3 0.000000 0.000000 0.004245 0.00000
(ATOM LINES ARE NOT SHOWN.)
END
