HEADER VIRAL PROTEIN 17-OCT-16 5TOH TITLE CRYSTAL STRUCTURE OF THE MARBURG VIRUS VP35 OLIGOMERIZATION DOMAIN I2 COMPND MOL_ID: 1; COMPND 2 MOLECULE: POLYMERASE COFACTOR VP35; COMPND 3 CHAIN: A, B, C; COMPND 4 FRAGMENT: UNP RESIDUES 60-130; COMPND 5 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: LAKE VICTORIA MARBURGVIRUS (STRAIN MUSOKE-80); SOURCE 3 ORGANISM_COMMON: MARV; SOURCE 4 ORGANISM_TAXID: 33727; SOURCE 5 STRAIN: MUSOKE-80; SOURCE 6 GENE: VP35; SOURCE 7 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 8 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS POLYMERASE COFACTOR, COILED COIL, OLIGOMERIZATION, TRIMER, VIRAL KEYWDS 2 PROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR J.F.BRUHN,R.N.KIRCHDOERFER,I.J.TICKLE,G.BRICOGNE,E.O.SAPHIRE REVDAT 8 06-MAR-24 5TOH 1 REMARK REVDAT 7 04-DEC-19 5TOH 1 REMARK REVDAT 6 27-SEP-17 5TOH 1 REMARK REVDAT 5 08-FEB-17 5TOH 1 JRNL REVDAT 4 11-JAN-17 5TOH 1 JRNL REVDAT 3 30-NOV-16 5TOH 1 JRNL REVDAT 2 23-NOV-16 5TOH 1 TITLE REVDAT 1 09-NOV-16 5TOH 0 JRNL AUTH J.F.BRUHN,R.N.KIRCHDOERFER,S.M.URATA,S.LI,I.J.TICKLE, JRNL AUTH 2 G.BRICOGNE,E.O.SAPHIRE JRNL TITL CRYSTAL STRUCTURE OF THE MARBURG VIRUS VP35 OLIGOMERIZATION JRNL TITL 2 DOMAIN. JRNL REF J. VIROL. V. 91 2017 JRNL REFN ESSN 1098-5514 JRNL PMID 27847355 JRNL DOI 10.1128/JVI.01085-16 REMARK 2 REMARK 2 RESOLUTION. 2.01 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : BUSTER 2.11.7 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) : 2.01 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 53.02 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 42.3 REMARK 3 NUMBER OF REFLECTIONS : 7657 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) : 0.241 REMARK 3 R VALUE (WORKING SET) : 0.239 REMARK 3 FREE R VALUE : 0.266 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.920 REMARK 3 FREE R VALUE TEST SET COUNT : 377 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) : 2.01 REMARK 3 BIN RESOLUTION RANGE LOW (ANGSTROMS) : 2.25 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 4.06 REMARK 3 REFLECTIONS IN BIN (WORKING + TEST SET) : 207 REMARK 3 BIN R VALUE (WORKING + TEST SET) : NULL REMARK 3 REFLECTIONS IN BIN (WORKING SET) : 198 REMARK 3 BIN R VALUE (WORKING SET) : 0.2400 REMARK 3 BIN FREE R VALUE : 0.2380 REMARK 3 BIN FREE R VALUE TEST SET SIZE (%) : 4.35 REMARK 3 BIN FREE R VALUE TEST SET COUNT : 9 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 : 1417 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 0 REMARK 3 SOLVENT ATOMS : 26 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 41.60 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 45.76 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 4.16650 REMARK 3 B22 (A**2) : -1.50600 REMARK 3 B33 (A**2) : -2.66050 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : 1.24920 REMARK 3 B23 (A**2) : 0.00000 REMARK 3 REMARK 3 ESTIMATED COORDINATE ERROR. REMARK 3 ESD FROM LUZZATI PLOT (A) : 0.480 REMARK 3 DPI (BLOW EQ-10) BASED ON R VALUE (A) : 0.540 REMARK 3 DPI (BLOW EQ-9) BASED ON FREE R VALUE (A) : 0.302 REMARK 3 DPI (CRUICKSHANK) BASED ON R VALUE (A) : NULL REMARK 3 DPI (CRUICKSHANK) BASED ON FREE R VALUE (A) : NULL 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 : 0.904 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.897 REMARK 3 REMARK 3 NUMBER OF GEOMETRIC FUNCTION TERMS DEFINED : 15 REMARK 3 TERM COUNT WEIGHT FUNCTION. REMARK 3 BOND LENGTHS : 2920 ; 2.000 ; HARMONIC REMARK 3 BOND ANGLES : 5328 ; 2.000 ; HARMONIC REMARK 3 TORSION ANGLES : 685 ; 2.000 ; SINUSOIDAL REMARK 3 TRIGONAL CARBON PLANES : 41 ; 2.000 ; HARMONIC REMARK 3 GENERAL PLANES : 412 ; 5.000 ; HARMONIC REMARK 3 ISOTROPIC THERMAL FACTORS : 2920 ; 20.000 ; HARMONIC REMARK 3 BAD NON-BONDED CONTACTS : 3 ; 5.000 ; SEMIHARMONIC REMARK 3 IMPROPER TORSIONS : NULL ; NULL ; NULL REMARK 3 PSEUDOROTATION ANGLES : NULL ; NULL ; NULL REMARK 3 CHIRAL IMPROPER TORSION : 215 ; 5.000 ; SEMIHARMONIC REMARK 3 SUM OF OCCUPANCIES : NULL ; NULL ; NULL 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 : 3007 ; 4.000 ; SEMIHARMONIC REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES. REMARK 3 BOND LENGTHS (A) : 0.009 REMARK 3 BOND ANGLES (DEGREES) : 0.96 REMARK 3 PEPTIDE OMEGA TORSION ANGLES (DEGREES) : 4.46 REMARK 3 OTHER TORSION ANGLES (DEGREES) : 15.13 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 5TOH COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 24-OCT-16. REMARK 100 THE DEPOSITION ID IS D_1000223343. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 14-MAR-14 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 6.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : APS REMARK 200 BEAMLINE : 23-ID-D REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.0332 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS PILATUS3 6M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : AIMLESS, STARANISO REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 7658 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.010 REMARK 200 RESOLUTION RANGE LOW (A) : 53.020 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 42.1 REMARK 200 DATA REDUNDANCY : 2.200 REMARK 200 R MERGE (I) : 0.13900 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 8.3000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.01 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.12 REMARK 200 COMPLETENESS FOR SHELL (%) : 2.4 REMARK 200 DATA REDUNDANCY IN SHELL : 2.10 REMARK 200 R MERGE FOR SHELL (I) : 1.00900 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 1.000 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: AB INITIO PHASING REMARK 200 SOFTWARE USED: MR-ROSETTA REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 54.97 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.73 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 100 MM SODIUM CACODYLATE PH 6.5, 100 REMARK 280 MM MG-ACETATE AND 18% 2-METHYL-2,4-PENTANEDIOL (MPD), CRYO- REMARK 280 PROTECTED BY ADDITION OF 25% ETHYLENE GLYCOL, VAPOR DIFFUSION, REMARK 280 SITTING DROP, TEMPERATURE 295.5K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: I 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+1/2 REMARK 290 4555 -X+1/2,Y+1/2,-Z+1/2 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 23.97772 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 17.50000 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 50.75986 REMARK 290 SMTRY1 4 -1.000000 0.000000 0.000000 23.97772 REMARK 290 SMTRY2 4 0.000000 1.000000 0.000000 17.50000 REMARK 290 SMTRY3 4 0.000000 0.000000 -1.000000 50.75986 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: 5200 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 12300 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -50.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, B, C 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 LEU A 53 REMARK 465 LYS A 54 REMARK 465 MET A 55 REMARK 465 GLY A 56 REMARK 465 ARG A 57 REMARK 465 THR A 58 REMARK 465 LEU A 59 REMARK 465 GLU A 60 REMARK 465 ALA A 61 REMARK 465 ILE A 62 REMARK 465 SER A 63 REMARK 465 LYS A 64 REMARK 465 GLY A 65 REMARK 465 MET A 66 REMARK 465 SER A 67 REMARK 465 GLU A 68 REMARK 465 MET A 69 REMARK 465 LEU A 70 REMARK 465 ALA A 71 REMARK 465 LYS A 72 REMARK 465 ALA B 71 REMARK 465 LYS B 72 REMARK 465 GLY C 1 REMARK 465 MET C 55 REMARK 465 GLY C 56 REMARK 465 ARG C 57 REMARK 465 THR C 58 REMARK 465 LEU C 59 REMARK 465 GLU C 60 REMARK 465 ALA C 61 REMARK 465 ILE C 62 REMARK 465 SER C 63 REMARK 465 LYS C 64 REMARK 465 GLY C 65 REMARK 465 MET C 66 REMARK 465 SER C 67 REMARK 465 GLU C 68 REMARK 465 MET C 69 REMARK 465 LEU C 70 REMARK 465 ALA C 71 REMARK 465 LYS C 72 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 ASP B 2 -78.79 -101.34 REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 5TOI RELATED DB: PDB DBREF 5TOH A 2 72 UNP P35259 VP35_MABVM 60 130 DBREF 5TOH B 2 72 UNP P35259 VP35_MABVM 60 130 DBREF 5TOH C 2 72 UNP P35259 VP35_MABVM 60 130 SEQADV 5TOH GLY A 1 UNP P35259 EXPRESSION TAG SEQADV 5TOH GLY B 1 UNP P35259 EXPRESSION TAG SEQADV 5TOH GLY C 1 UNP P35259 EXPRESSION TAG SEQRES 1 A 72 GLY ASP ILE ILE TRP ASP GLN LEU ILE VAL LYS ARG THR SEQRES 2 A 72 LEU ALA ASP LEU LEU ILE PRO ILE ASN ARG GLN ILE SER SEQRES 3 A 72 ASP ILE GLN SER THR LEU SER GLU VAL THR THR ARG VAL SEQRES 4 A 72 HIS GLU ILE GLU ARG GLN LEU HIS GLU ILE THR PRO VAL SEQRES 5 A 72 LEU LYS MET GLY ARG THR LEU GLU ALA ILE SER LYS GLY SEQRES 6 A 72 MET SER GLU MET LEU ALA LYS SEQRES 1 B 72 GLY ASP ILE ILE TRP ASP GLN LEU ILE VAL LYS ARG THR SEQRES 2 B 72 LEU ALA ASP LEU LEU ILE PRO ILE ASN ARG GLN ILE SER SEQRES 3 B 72 ASP ILE GLN SER THR LEU SER GLU VAL THR THR ARG VAL SEQRES 4 B 72 HIS GLU ILE GLU ARG GLN LEU HIS GLU ILE THR PRO VAL SEQRES 5 B 72 LEU LYS MET GLY ARG THR LEU GLU ALA ILE SER LYS GLY SEQRES 6 B 72 MET SER GLU MET LEU ALA LYS SEQRES 1 C 72 GLY ASP ILE ILE TRP ASP GLN LEU ILE VAL LYS ARG THR SEQRES 2 C 72 LEU ALA ASP LEU LEU ILE PRO ILE ASN ARG GLN ILE SER SEQRES 3 C 72 ASP ILE GLN SER THR LEU SER GLU VAL THR THR ARG VAL SEQRES 4 C 72 HIS GLU ILE GLU ARG GLN LEU HIS GLU ILE THR PRO VAL SEQRES 5 C 72 LEU LYS MET GLY ARG THR LEU GLU ALA ILE SER LYS GLY SEQRES 6 C 72 MET SER GLU MET LEU ALA LYS FORMUL 4 HOH *26(H2 O) HELIX 1 AA1 ASP A 2 LEU A 18 1 17 HELIX 2 AA2 LEU A 18 GLU A 48 1 31 HELIX 3 AA3 ASP B 2 LEU B 18 1 17 HELIX 4 AA4 LEU B 18 LEU B 70 1 53 HELIX 5 AA5 ILE C 3 ILE C 49 1 47 CRYST1 75.690 35.000 105.240 90.00 105.28 90.00 I 1 2 1 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 0.013212 0.000000 0.003609 0.00000 SCALE2 0.000000 0.028571 0.000000 0.00000 SCALE3 0.000000 0.000000 0.009850 0.00000