HEADER PROTEIN BINDING 28-JUL-17 5OMD
TITLE CRYSTAL STRUCTURE OF S. CEREVISIAE DDC2 N-TERMINAL COILED-COIL DOMAIN
COMPND MOL_ID: 1;
COMPND 2 MOLECULE: DNA DAMAGE CHECKPOINT PROTEIN LCD1;
COMPND 3 CHAIN: A;
COMPND 4 FRAGMENT: UNP RESIDUES 73-136;
COMPND 5 SYNONYM: DNA DAMAGE CHECKPOINT PROTEIN 2,LETHAL,CHECKPOINT-DEFECTIVE,
COMPND 6 DNA DAMAGE-SENSITIVE PROTEIN 1;
COMPND 7 ENGINEERED: YES
SOURCE MOL_ID: 1;
SOURCE 2 ORGANISM_SCIENTIFIC: SACCHAROMYCES CEREVISIAE (STRAIN ATCC 204508 /
SOURCE 3 S288C);
SOURCE 4 ORGANISM_COMMON: BAKER'S YEAST;
SOURCE 5 ORGANISM_TAXID: 559292;
SOURCE 6 GENE: LCD1, DDC2, PIE1, YDR499W;
SOURCE 7 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21(DE3);
SOURCE 8 EXPRESSION_SYSTEM_TAXID: 469008;
SOURCE 9 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID;
SOURCE 10 EXPRESSION_SYSTEM_PLASMID: POPINF
KEYWDS COILED-COIL, DIMERIZATION, PROTEIN BINDING
EXPDTA X-RAY DIFFRACTION
AUTHOR I.DESHPANDE,A.SEEBER,K.SHIMADA,J.J.KEUSCH,H.GUT,S.M.GASSER
REVDAT 3 17-JAN-24 5OMD 1 REMARK
REVDAT 2 01-NOV-17 5OMD 1 JRNL
REVDAT 1 25-OCT-17 5OMD 0
JRNL AUTH I.DESHPANDE,A.SEEBER,K.SHIMADA,J.J.KEUSCH,H.GUT,S.M.GASSER
JRNL TITL STRUCTURAL BASIS OF MEC1-DDC2-RPA ASSEMBLY AND ACTIVATION ON
JRNL TITL 2 SINGLE-STRANDED DNA AT SITES OF DAMAGE.
JRNL REF MOL. CELL V. 68 431 2017
JRNL REFN ISSN 1097-4164
JRNL PMID 29033322
JRNL DOI 10.1016/J.MOLCEL.2017.09.019
REMARK 2
REMARK 2 RESOLUTION. 2.10 ANGSTROMS.
REMARK 3
REMARK 3 REFINEMENT.
REMARK 3 PROGRAM : BUSTER 2.11.5
REMARK 3 AUTHORS : BRICOGNE,BLANC,BRANDL,FLENSBURG,KELLER,
REMARK 3 : PACIOREK,ROVERSI,SHARFF,SMART,VONRHEIN,
REMARK 3 : WOMACK,MATTHEWS,TEN EYCK,TRONRUD
REMARK 3
REMARK 3 DATA USED IN REFINEMENT.
REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.10
REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 38.98
REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000
REMARK 3 COMPLETENESS FOR RANGE (%) : 99.9
REMARK 3 NUMBER OF REFLECTIONS : 4644
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) : 0.233
REMARK 3 R VALUE (WORKING SET) : 0.228
REMARK 3 FREE R VALUE : 0.270
REMARK 3 FREE R VALUE TEST SET SIZE (%) : 12.020
REMARK 3 FREE R VALUE TEST SET COUNT : 558
REMARK 3 ESTIMATED ERROR OF FREE R VALUE : NULL
REMARK 3
REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN.
REMARK 3 TOTAL NUMBER OF BINS USED : 5
REMARK 3 BIN RESOLUTION RANGE HIGH (ANGSTROMS) : 2.10
REMARK 3 BIN RESOLUTION RANGE LOW (ANGSTROMS) : 2.35
REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 99.87
REMARK 3 REFLECTIONS IN BIN (WORKING + TEST SET) : 1256
REMARK 3 BIN R VALUE (WORKING + TEST SET) : 0.2268
REMARK 3 REFLECTIONS IN BIN (WORKING SET) : 1105
REMARK 3 BIN R VALUE (WORKING SET) : 0.2217
REMARK 3 BIN FREE R VALUE : 0.2628
REMARK 3 BIN FREE R VALUE TEST SET SIZE (%) : 12.02
REMARK 3 BIN FREE R VALUE TEST SET COUNT : 151
REMARK 3 ESTIMATED ERROR OF BIN FREE R VALUE : NULL
REMARK 3
REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT.
REMARK 3 PROTEIN ATOMS : 506
REMARK 3 NUCLEIC ACID ATOMS : 0
REMARK 3 HETEROGEN ATOMS : 0
REMARK 3 SOLVENT ATOMS : 45
REMARK 3
REMARK 3 B VALUES.
REMARK 3 FROM WILSON PLOT (A**2) : 35.69
REMARK 3 MEAN B VALUE (OVERALL, A**2) : 51.81
REMARK 3 OVERALL ANISOTROPIC B VALUE.
REMARK 3 B11 (A**2) : 5.35160
REMARK 3 B22 (A**2) : -2.65710
REMARK 3 B33 (A**2) : -2.69450
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 COORDINATE ERROR.
REMARK 3 ESD FROM LUZZATI PLOT (A) : 0.347
REMARK 3 DPI (BLOW EQ-10) BASED ON R VALUE (A) : 0.269
REMARK 3 DPI (BLOW EQ-9) BASED ON FREE R VALUE (A) : 0.209
REMARK 3 DPI (CRUICKSHANK) BASED ON R VALUE (A) : 0.231
REMARK 3 DPI (CRUICKSHANK) BASED ON FREE R VALUE (A) : 0.196
REMARK 3
REMARK 3 REFERENCES: BLOW, D. (2002) ACTA CRYST D58, 792-797
REMARK 3 CRUICKSHANK, D.W.J. (1999) ACTA CRYST D55, 583-601
REMARK 3
REMARK 3 CORRELATION COEFFICIENTS.
REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.941
REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.946
REMARK 3
REMARK 3 NUMBER OF GEOMETRIC FUNCTION TERMS DEFINED : 15
REMARK 3 TERM COUNT WEIGHT FUNCTION.
REMARK 3 BOND LENGTHS : 521 ; 2.000 ; HARMONIC
REMARK 3 BOND ANGLES : 692 ; 2.000 ; HARMONIC
REMARK 3 TORSION ANGLES : 214 ; 2.000 ; SINUSOIDAL
REMARK 3 TRIGONAL CARBON PLANES : 22 ; 2.000 ; HARMONIC
REMARK 3 GENERAL PLANES : 68 ; 5.000 ; HARMONIC
REMARK 3 ISOTROPIC THERMAL FACTORS : 521 ; 20.000 ; HARMONIC
REMARK 3 BAD NON-BONDED CONTACTS : NULL ; NULL ; NULL
REMARK 3 IMPROPER TORSIONS : NULL ; NULL ; NULL
REMARK 3 PSEUDOROTATION ANGLES : NULL ; NULL ; NULL
REMARK 3 CHIRAL IMPROPER TORSION : 64 ; 5.000 ; SEMIHARMONIC
REMARK 3 SUM OF OCCUPANCIES : 1 ; 1.000 ; HARMONIC
REMARK 3 UTILITY DISTANCES : NULL ; NULL ; NULL
REMARK 3 UTILITY ANGLES : NULL ; NULL ; NULL
REMARK 3 UTILITY TORSION : NULL ; NULL ; NULL
REMARK 3 IDEAL-DIST CONTACT TERM : 663 ; 4.000 ; SEMIHARMONIC
REMARK 3
REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES.
REMARK 3 BOND LENGTHS (A) : 0.010
REMARK 3 BOND ANGLES (DEGREES) : 1.15
REMARK 3 PEPTIDE OMEGA TORSION ANGLES (DEGREES) : 1.96
REMARK 3 OTHER TORSION ANGLES (DEGREES) : 20.35
REMARK 3
REMARK 3 TLS DETAILS
REMARK 3 NUMBER OF TLS GROUPS : 1
REMARK 3
REMARK 3 TLS GROUP : 1
REMARK 3 SELECTION: { A|* }
REMARK 3 ORIGIN FOR THE GROUP (A): 28.4228 5.3861 14.1176
REMARK 3 T TENSOR
REMARK 3 T11: -0.0950 T22: -0.2433
REMARK 3 T33: 0.0678 T12: 0.0124
REMARK 3 T13: -0.0412 T23: 0.0653
REMARK 3 L TENSOR
REMARK 3 L11: 16.0356 L22: 0.4724
REMARK 3 L33: 1.0497 L12: 0.6179
REMARK 3 L13: 0.4864 L23: 0.2653
REMARK 3 S TENSOR
REMARK 3 S11: 0.2186 S12: 0.3374 S13: -0.6490
REMARK 3 S21: 0.0718 S22: -0.1014 S23: -0.3835
REMARK 3 S31: 0.0526 S32: 0.2044 S33: -0.1172
REMARK 3
REMARK 3 OTHER REFINEMENT REMARKS: NULL
REMARK 4
REMARK 4 5OMD COMPLIES WITH FORMAT V. 3.30, 13-JUL-11
REMARK 100
REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 28-JUL-17.
REMARK 100 THE DEPOSITION ID IS D_1200006038.
REMARK 200
REMARK 200 EXPERIMENTAL DETAILS
REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION
REMARK 200 DATE OF DATA COLLECTION : 06-MAY-13
REMARK 200 TEMPERATURE (KELVIN) : 100
REMARK 200 PH : 8.5
REMARK 200 NUMBER OF CRYSTALS USED : 1
REMARK 200
REMARK 200 SYNCHROTRON (Y/N) : Y
REMARK 200 RADIATION SOURCE : SLS
REMARK 200 BEAMLINE : X06DA
REMARK 200 X-RAY GENERATOR MODEL : NULL
REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M
REMARK 200 WAVELENGTH OR RANGE (A) : 1.00005
REMARK 200 MONOCHROMATOR : NULL
REMARK 200 OPTICS : NULL
REMARK 200
REMARK 200 DETECTOR TYPE : PIXEL
REMARK 200 DETECTOR MANUFACTURER : DECTRIS PILATUS 2M
REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS
REMARK 200 DATA SCALING SOFTWARE : XSCALE
REMARK 200
REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 4644
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 (%) : 99.8
REMARK 200 DATA REDUNDANCY : 6.080
REMARK 200 R MERGE (I) : NULL
REMARK 200 R SYM (I) : 0.09000
REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 13.2300
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) : 2.15
REMARK 200 COMPLETENESS FOR SHELL (%) : 98.5
REMARK 200 DATA REDUNDANCY IN SHELL : 5.72
REMARK 200 R MERGE FOR SHELL (I) : NULL
REMARK 200 R SYM FOR SHELL (I) : 0.85600
REMARK 200 <I/SIGMA(I)> FOR SHELL : 2.190
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: 1A92
REMARK 200
REMARK 200 REMARK: NULL
REMARK 280
REMARK 280 CRYSTAL
REMARK 280 SOLVENT CONTENT, VS (%): 46.98
REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.32
REMARK 280
REMARK 280 CRYSTALLIZATION CONDITIONS: 0.1 M TRIS-HCL, 24% PEG 400, PH 8.5,
REMARK 280 VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 293K
REMARK 290
REMARK 290 CRYSTALLOGRAPHIC SYMMETRY
REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 2 2 21
REMARK 290
REMARK 290 SYMOP SYMMETRY
REMARK 290 NNNMMM OPERATOR
REMARK 290 1555 X,Y,Z
REMARK 290 2555 -X,-Y,Z+1/2
REMARK 290 3555 -X,Y,-Z+1/2
REMARK 290 4555 X,-Y,-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 15.40000
REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000
REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 0.00000
REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 15.40000
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 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: DIMERIC
REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC
REMARK 350 SOFTWARE USED: PISA
REMARK 350 TOTAL BURIED SURFACE AREA: 2610 ANGSTROM**2
REMARK 350 SURFACE AREA OF THE COMPLEX: 9770 ANGSTROM**2
REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -29.0 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 350 BIOMT1 2 1.000000 0.000000 0.000000 0.00000
REMARK 350 BIOMT2 2 0.000000 -1.000000 0.000000 19.89000
REMARK 350 BIOMT3 2 0.000000 0.000000 -1.000000 30.80000
REMARK 375
REMARK 375 SPECIAL POSITION
REMARK 375 THE FOLLOWING ATOMS ARE FOUND TO BE WITHIN 0.15 ANGSTROMS
REMARK 375 OF A SYMMETRY RELATED ATOM AND ARE ASSUMED TO BE ON SPECIAL
REMARK 375 POSITIONS.
REMARK 375
REMARK 375 ATOM RES CSSEQI
REMARK 375 HOH A 209 LIES ON A SPECIAL POSITION.
REMARK 375 HOH A 230 LIES ON A SPECIAL POSITION.
REMARK 375 HOH A 242 LIES ON A SPECIAL POSITION.
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 71
REMARK 465 ARG A 133
REMARK 465 GLY A 134
REMARK 465 LYS A 135
REMARK 465 SER A 136
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 MET A 130 56.65 -90.86
REMARK 500 GLU A 131 60.39 -150.44
REMARK 500
REMARK 500 REMARK: NULL
DBREF 5OMD A 73 136 UNP Q04377 LCD1_YEAST 73 136
SEQADV 5OMD GLY A 71 UNP Q04377 EXPRESSION TAG
SEQADV 5OMD PRO A 72 UNP Q04377 EXPRESSION TAG
SEQRES 1 A 66 GLY PRO GLY GLU ALA SER MET LEU ARG ASP LYS ILE ASN
SEQRES 2 A 66 PHE LEU ASN ILE GLU ARG GLU LYS GLU LYS ASN ILE GLN
SEQRES 3 A 66 ALA VAL LYS VAL ASN GLU LEU GLN VAL LYS HIS LEU GLN
SEQRES 4 A 66 GLU LEU ALA LYS LEU LYS GLN GLU LEU GLN LYS LEU GLU
SEQRES 5 A 66 ASP GLU LYS LYS PHE LEU GLN MET GLU ALA ARG GLY LYS
SEQRES 6 A 66 SER
FORMUL 2 HOH *45(H2 O)
HELIX 1 AA1 PRO A 72 MET A 130 1 59
CRYST1 116.940 19.890 30.800 90.00 90.00 90.00 P 2 2 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 0.008551 0.000000 0.000000 0.00000
SCALE2 0.000000 0.050277 0.000000 0.00000
SCALE3 0.000000 0.000000 0.032468 0.00000