HEADER REPLICATION 13-JUN-17 5O8K TITLE CRYSTAL STRUCTURE OF MAMMALIAN REV7 IN COMPLEX WITH REV3 1875-1895 COMPND MOL_ID: 1; COMPND 2 MOLECULE: MITOTIC SPINDLE ASSEMBLY CHECKPOINT PROTEIN MAD2B; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: MITOTIC ARREST DEFICIENT 2-LIKE PROTEIN 2,MAD2-LIKE PROTEIN COMPND 5 2; COMPND 6 ENGINEERED: YES; COMPND 7 MUTATION: YES; COMPND 8 MOL_ID: 2; COMPND 9 MOLECULE: DNA POLYMERASE ZETA CATALYTIC SUBUNIT; COMPND 10 CHAIN: B; COMPND 11 SYNONYM: PROTEIN REVERSIONLESS 3-LIKE,HREV3; COMPND 12 EC: 2.7.7.7; COMPND 13 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: MUS MUSCULUS; SOURCE 3 ORGANISM_COMMON: HOUSE MOUSE; SOURCE 4 ORGANISM_TAXID: 10090; SOURCE 5 GENE: MAD2L2, MAD2B, REV7; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 511693; SOURCE 8 EXPRESSION_SYSTEM_STRAIN: BL21; SOURCE 9 MOL_ID: 2; SOURCE 10 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 11 ORGANISM_COMMON: HUMAN; SOURCE 12 ORGANISM_TAXID: 9606; SOURCE 13 GENE: REV3L, POLZ, REV3; SOURCE 14 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 15 EXPRESSION_SYSTEM_TAXID: 511693; SOURCE 16 EXPRESSION_SYSTEM_STRAIN: BL21 KEYWDS REV7, MAD2L2, DNA POLYMERASE ZETA, DNA REPLICATION, REPLICATION EXPDTA X-RAY DIFFRACTION AUTHOR S.EMAMZADAH,L.TROPIA,F.HUBER,T.HALAZONETIS REVDAT 2 17-JAN-24 5O8K 1 REMARK REVDAT 1 27-JUN-18 5O8K 0 JRNL AUTH S.EMAMZADAH,L.TROPIA,F.HUBER,T.HALAZONETIS JRNL TITL CRYSTAL STRUCTURE OF MAMMALIAN REV7 IN COMPLEX WITH REV3 JRNL TITL 2 1875-1895 JRNL REF TO BE PUBLISHED JRNL REFN REMARK 2 REMARK 2 RESOLUTION. 1.80 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : CNS REMARK 3 AUTHORS : BRUNGER,ADAMS,CLORE,DELANO,GROS,GROSSE- REMARK 3 : KUNSTLEVE,JIANG,KUSZEWSKI,NILGES,PANNU, REMARK 3 : READ,RICE,SIMONSON,WARREN REMARK 3 REMARK 3 REFINEMENT TARGET : NULL REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.80 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 70.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 DATA CUTOFF HIGH (ABS(F)) : NULL REMARK 3 DATA CUTOFF LOW (ABS(F)) : NULL REMARK 3 COMPLETENESS (WORKING+TEST) (%) : 96.4 REMARK 3 NUMBER OF REFLECTIONS : 20408 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 SET) : 0.255 REMARK 3 FREE R VALUE : 0.289 REMARK 3 FREE R VALUE TEST SET SIZE (%) : NULL REMARK 3 FREE R VALUE TEST SET COUNT : NULL 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 : NULL REMARK 3 BIN RESOLUTION RANGE HIGH (A) : NULL REMARK 3 BIN RESOLUTION RANGE LOW (A) : NULL REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : NULL REMARK 3 REFLECTIONS IN BIN (WORKING SET) : NULL REMARK 3 BIN R VALUE (WORKING SET) : NULL REMARK 3 BIN FREE R VALUE : NULL REMARK 3 BIN FREE R VALUE TEST SET SIZE (%) : NULL REMARK 3 BIN FREE R VALUE TEST SET COUNT : NULL 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 : 1814 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 0 REMARK 3 SOLVENT ATOMS : 37 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : NULL 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 COORDINATE ERROR. REMARK 3 ESD FROM LUZZATI PLOT (A) : NULL REMARK 3 ESD FROM SIGMAA (A) : NULL REMARK 3 LOW RESOLUTION CUTOFF (A) : NULL REMARK 3 REMARK 3 CROSS-VALIDATED ESTIMATED COORDINATE ERROR. REMARK 3 ESD FROM C-V LUZZATI PLOT (A) : NULL REMARK 3 ESD FROM C-V SIGMAA (A) : NULL REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES. REMARK 3 BOND LENGTHS (A) : NULL REMARK 3 BOND ANGLES (DEGREES) : NULL REMARK 3 DIHEDRAL ANGLES (DEGREES) : NULL REMARK 3 IMPROPER ANGLES (DEGREES) : NULL REMARK 3 REMARK 3 ISOTROPIC THERMAL MODEL : NULL REMARK 3 REMARK 3 ISOTROPIC THERMAL FACTOR RESTRAINTS. RMS SIGMA REMARK 3 MAIN-CHAIN BOND (A**2) : NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE (A**2) : NULL ; NULL REMARK 3 SIDE-CHAIN BOND (A**2) : NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE (A**2) : NULL ; NULL REMARK 3 REMARK 3 BULK SOLVENT MODELING. REMARK 3 METHOD USED : NULL REMARK 3 KSOL : NULL REMARK 3 BSOL : NULL REMARK 3 REMARK 3 NCS MODEL : NULL REMARK 3 REMARK 3 NCS RESTRAINTS. RMS SIGMA/WEIGHT REMARK 3 GROUP 1 POSITIONAL (A) : NULL ; NULL REMARK 3 GROUP 1 B-FACTOR (A**2) : NULL ; NULL REMARK 3 REMARK 3 PARAMETER FILE 1 : NULL REMARK 3 TOPOLOGY FILE 1 : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 5O8K COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 13-JUN-17. REMARK 100 THE DEPOSITION ID IS D_1200005357. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 13-NOV-11 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 7.5 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) : 0.93340 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 : IMOSFLM REMARK 200 DATA SCALING SOFTWARE : SCALA REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 20408 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.800 REMARK 200 RESOLUTION RANGE LOW (A) : 70.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 96.4 REMARK 200 DATA REDUNDANCY : 4.300 REMARK 200 R MERGE (I) : 0.11900 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 7.3000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.80 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.90 REMARK 200 COMPLETENESS FOR SHELL (%) : 99.6 REMARK 200 DATA REDUNDANCY IN SHELL : 4.60 REMARK 200 R MERGE FOR SHELL (I) : 0.32200 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 3.500 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: NULL REMARK 200 SOFTWARE USED: PHASER REMARK 200 STARTING MODEL: 3ABD REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 42.37 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.13 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 25% PEG 2000 MME, 0.8M SODIUM FORMATE, REMARK 280 0.1M TRIS-HCL PH 7.5, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE REMARK 280 293K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 32 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -Y,X-Y,Z+2/3 REMARK 290 3555 -X+Y,-X,Z+1/3 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 28.57867 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 14.28933 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: 2220 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 11230 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -18.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, B 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 MET A 1 REMARK 465 THR A 2 REMARK 465 THR A 3 REMARK 465 LEU A 4 REMARK 465 THR A 5 REMARK 465 ARG A 6 REMARK 465 GLN A 7 REMARK 465 SER A 211 REMARK 465 MET B 1871 REMARK 465 GLY B 1872 REMARK 465 ARG B 1873 REMARK 465 THR B 1874 REMARK 465 ASP B 1896 REMARK 465 HIS B 1897 REMARK 465 ASP B 1898 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 SER A 112 101.44 -53.29 REMARK 500 ASP A 113 -93.28 -160.99 REMARK 500 ASP A 168 -15.08 70.38 REMARK 500 ASP A 183 -104.90 70.54 REMARK 500 PRO A 184 -162.09 -111.17 REMARK 500 REMARK 500 REMARK: NULL DBREF 5O8K A 1 211 UNP Q9D752 MD2L2_MOUSE 1 211 DBREF 5O8K B 1873 1898 UNP O60673 REV3L_HUMAN 1873 1898 SEQADV 5O8K SER A 11 UNP Q9D752 PHE 11 ENGINEERED MUTATION SEQADV 5O8K ALA A 12 UNP Q9D752 GLY 12 ENGINEERED MUTATION SEQADV 5O8K LYS A 132 UNP Q9D752 VAL 132 ENGINEERED MUTATION SEQADV 5O8K VAL A 133 UNP Q9D752 CYS 133 ENGINEERED MUTATION SEQADV 5O8K LYS A 135 UNP Q9D752 ALA 135 ENGINEERED MUTATION SEQADV 5O8K MET B 1871 UNP O60673 INITIATING METHIONINE SEQADV 5O8K GLY B 1872 UNP O60673 EXPRESSION TAG SEQRES 1 A 211 MET THR THR LEU THR ARG GLN ASP LEU ASN SER ALA GLN SEQRES 2 A 211 VAL VAL ALA ASP VAL LEU SER GLU PHE LEU GLU VAL ALA SEQRES 3 A 211 VAL HIS LEU ILE LEU TYR VAL ARG GLU VAL TYR PRO VAL SEQRES 4 A 211 GLY ILE PHE GLN LYS ARG LYS LYS TYR ASN VAL PRO VAL SEQRES 5 A 211 GLN MET SER CYS HIS PRO GLU LEU ASN GLN TYR ILE GLN SEQRES 6 A 211 ASP THR LEU HIS CYS VAL LYS PRO LEU LEU GLU LYS ASN SEQRES 7 A 211 ASP VAL GLU LYS VAL VAL VAL VAL ILE LEU ASP LYS GLU SEQRES 8 A 211 HIS ARG PRO VAL GLU LYS PHE VAL PHE GLU ILE THR GLN SEQRES 9 A 211 PRO PRO LEU LEU SER ILE ASN SER ASP SER LEU LEU SER SEQRES 10 A 211 HIS VAL GLU GLN LEU LEU ARG ALA PHE ILE LEU LYS ILE SEQRES 11 A 211 SER LYS VAL ASP LYS VAL LEU ASP HIS ASN PRO PRO GLY SEQRES 12 A 211 CYS THR PHE THR VAL LEU VAL HIS THR ARG GLU ALA ALA SEQRES 13 A 211 THR ARG ASN MET GLU LYS ILE GLN VAL ILE LYS ASP PHE SEQRES 14 A 211 PRO TRP ILE LEU ALA ASP GLU GLN ASP VAL HIS MET HIS SEQRES 15 A 211 ASP PRO ARG LEU ILE PRO LEU LYS THR MET THR SER ASP SEQRES 16 A 211 ILE LEU LYS MET GLN LEU TYR VAL GLU GLU ARG ALA HIS SEQRES 17 A 211 LYS ASN SER SEQRES 1 B 28 MET GLY ARG THR ALA ASN ILE LEU LYS PRO LEU MET SER SEQRES 2 B 28 PRO PRO SER ARG GLU GLU ILE MET ALA THR LEU LEU ASP SEQRES 3 B 28 HIS ASP FORMUL 3 HOH *37(H2 O) HELIX 1 AA1 ASN A 10 ARG A 34 1 25 HELIX 2 AA2 PRO A 38 GLY A 40 5 3 HELIX 3 AA3 HIS A 57 LYS A 77 1 21 HELIX 4 AA4 ASP A 113 SER A 131 1 19 HELIX 5 AA5 LYS A 132 VAL A 136 5 5 HELIX 6 AA6 SER B 1886 LEU B 1895 1 10 SHEET 1 AA1 2 PHE A 42 LYS A 47 0 SHEET 2 AA1 2 VAL A 50 SER A 55 -1 O VAL A 52 N ARG A 45 SHEET 1 AA2 7 TRP A 171 LEU A 173 0 SHEET 2 AA2 7 ILE B1877 PRO B1880 -1 O LYS B1879 N ILE A 172 SHEET 3 AA2 7 THR A 145 THR A 152 -1 N VAL A 150 O LEU B1878 SHEET 4 AA2 7 VAL A 80 LEU A 88 -1 N GLU A 81 O HIS A 151 SHEET 5 AA2 7 PRO A 94 THR A 103 -1 O VAL A 95 N ILE A 87 SHEET 6 AA2 7 LYS A 198 GLU A 205 -1 O GLU A 204 N LYS A 97 SHEET 7 AA2 7 ARG A 185 MET A 192 -1 N ARG A 185 O GLU A 205 CISPEP 1 ASP A 183 PRO A 184 0 -0.56 CRYST1 69.014 69.014 42.868 90.00 90.00 120.00 P 32 3 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 0.014490 0.008366 0.000000 0.00000 SCALE2 0.000000 0.016731 0.000000 0.00000 SCALE3 0.000000 0.000000 0.023327 0.00000