HEADER VIRAL PROTEIN 06-MAY-14 4QB0 TITLE THE CRYSTAL STRUCTURE OF THE C-TERMINAL DOMAIN OF EBOLA (ZAIRE) TITLE 2 NUCLEOPROTEIN COMPND MOL_ID: 1; COMPND 2 MOLECULE: NUCLEOPROTEIN; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: NUCLEOCAPSID PROTEIN, PROTEIN N; COMPND 5 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: EBOLA VIRUS; SOURCE 3 ORGANISM_COMMON: ZEBOV; SOURCE 4 ORGANISM_TAXID: 128952; SOURCE 5 STRAIN: MAYINGA; SOURCE 6 GENE: NP; SOURCE 7 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 8 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 9 EXPRESSION_SYSTEM_STRAIN: BL21(DE3); SOURCE 10 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 11 EXPRESSION_SYSTEM_PLASMID: PARALLEL1-MBPHIS KEYWDS NEW FAMILY, EBOLA VIRUS VP40, VIRAL PROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR U.DEREWENDA,P.J.DZIUBANSKA,Z.S.DEREWENDA REVDAT 3 28-FEB-24 4QB0 1 SEQADV REVDAT 2 24-SEP-14 4QB0 1 JRNL REVDAT 1 10-SEP-14 4QB0 0 JRNL AUTH P.J.DZIUBANSKA,U.DEREWENDA,J.F.ELLENA,D.A.ENGEL, JRNL AUTH 2 Z.S.DEREWENDA JRNL TITL THE STRUCTURE OF THE C-TERMINAL DOMAIN OF THE ZAIRE JRNL TITL 2 EBOLAVIRUS NUCLEOPROTEIN. JRNL REF ACTA CRYSTALLOGR.,SECT.D V. 70 2420 2014 JRNL REFN ISSN 0907-4449 JRNL PMID 25195755 JRNL DOI 10.1107/S1399004714014710 REMARK 2 REMARK 2 RESOLUTION. 1.75 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX (PHENIX.REFINE: 1.8.4_1496) REMARK 3 AUTHORS : PAUL ADAMS,PAVEL AFONINE,VINCENT CHEN,IAN REMARK 3 : DAVIS,KRESHNA GOPAL,RALF GROSSE-KUNSTLEVE, REMARK 3 : LI-WEI HUNG,ROBERT IMMORMINO,TOM IOERGER, REMARK 3 : AIRLIE MCCOY,ERIK MCKEE,NIGEL MORIARTY, REMARK 3 : REETAL PAI,RANDY READ,JANE RICHARDSON, REMARK 3 : DAVID RICHARDSON,TOD ROMO,JIM SACCHETTINI, REMARK 3 : NICHOLAS SAUTER,JACOB SMITH,LAURENT REMARK 3 : STORONI,TOM TERWILLIGER,PETER ZWART REMARK 3 REMARK 3 REFINEMENT TARGET : ML REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.75 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 29.36 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.360 REMARK 3 COMPLETENESS FOR RANGE (%) : 97.5 REMARK 3 NUMBER OF REFLECTIONS : 9989 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.185 REMARK 3 R VALUE (WORKING SET) : 0.183 REMARK 3 FREE R VALUE : 0.225 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.900 REMARK 3 FREE R VALUE TEST SET COUNT : 489 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT (IN BINS). REMARK 3 BIN RESOLUTION RANGE COMPL. NWORK NFREE RWORK RFREE REMARK 3 1 29.3627 - 2.5242 1.00 3362 171 0.1649 0.1972 REMARK 3 2 2.5242 - 2.0037 1.00 3200 174 0.2034 0.2568 REMARK 3 3 2.0037 - 1.7504 0.93 2938 144 0.2393 0.3064 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : FLAT BULK SOLVENT MODEL REMARK 3 SOLVENT RADIUS : 1.11 REMARK 3 SHRINKAGE RADIUS : 0.90 REMARK 3 K_SOL : NULL REMARK 3 B_SOL : NULL REMARK 3 REMARK 3 ERROR ESTIMATES. REMARK 3 COORDINATE ERROR (MAXIMUM-LIKELIHOOD BASED) : 0.200 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 25.790 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 23.80 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 TWINNING INFORMATION. REMARK 3 FRACTION: NULL REMARK 3 OPERATOR: NULL REMARK 3 REMARK 3 DEVIATIONS FROM IDEAL VALUES. REMARK 3 RMSD COUNT REMARK 3 BOND : 0.013 834 REMARK 3 ANGLE : 1.315 1134 REMARK 3 CHIRALITY : 0.062 110 REMARK 3 PLANARITY : 0.008 150 REMARK 3 DIHEDRAL : 13.514 306 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : 2 REMARK 3 TLS GROUP : 1 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 645 THROUGH 684 ) REMARK 3 ORIGIN FOR THE GROUP (A): 31.9912 56.8149 25.3429 REMARK 3 T TENSOR REMARK 3 T11: 0.1597 T22: 0.1935 REMARK 3 T33: 0.1179 T12: 0.0194 REMARK 3 T13: 0.0234 T23: 0.0047 REMARK 3 L TENSOR REMARK 3 L11: 4.8931 L22: 5.9701 REMARK 3 L33: 4.0820 L12: 0.8914 REMARK 3 L13: 0.4446 L23: 0.6640 REMARK 3 S TENSOR REMARK 3 S11: 0.0111 S12: 0.0834 S13: 0.1024 REMARK 3 S21: 0.1860 S22: -0.0284 S23: 0.0959 REMARK 3 S31: -0.2110 S32: -0.2484 S33: 0.0370 REMARK 3 TLS GROUP : 2 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 685 THROUGH 739 ) REMARK 3 ORIGIN FOR THE GROUP (A): 30.2853 39.4062 15.9429 REMARK 3 T TENSOR REMARK 3 T11: 0.1243 T22: 0.1553 REMARK 3 T33: 0.1497 T12: 0.0116 REMARK 3 T13: -0.0156 T23: 0.0052 REMARK 3 L TENSOR REMARK 3 L11: 2.0010 L22: 4.6996 REMARK 3 L33: 4.8992 L12: 2.0606 REMARK 3 L13: -1.2795 L23: 0.2759 REMARK 3 S TENSOR REMARK 3 S11: -0.1935 S12: 0.0349 S13: -0.0292 REMARK 3 S21: -0.1510 S22: 0.1369 S23: 0.1577 REMARK 3 S31: 0.3130 S32: 0.1173 S33: 0.0430 REMARK 3 REMARK 3 NCS DETAILS REMARK 3 NUMBER OF NCS GROUPS : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 4QB0 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 13-MAY-14. REMARK 100 THE DEPOSITION ID IS D_1000085827. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 31-OCT-13 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : NULL REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : APS REMARK 200 BEAMLINE : 22-BM REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.0 REMARK 200 MONOCHROMATOR : DOUBLE CRYSTAL SI(220) REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : MARMOSAIC 225 MM CCD REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : HKL-2000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 9991 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.750 REMARK 200 RESOLUTION RANGE LOW (A) : 35.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : -3.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 97.7 REMARK 200 DATA REDUNDANCY : 6.300 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : 0.04900 REMARK 200 FOR THE DATA SET : 31.6000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.75 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.78 REMARK 200 COMPLETENESS FOR SHELL (%) : 82.2 REMARK 200 DATA REDUNDANCY IN SHELL : 3.20 REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : 0.29200 REMARK 200 FOR SHELL : 1.740 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: PHENIX REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 37.30 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 1.96 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 19.3% PEG3350, 0.05M MAGNESIUM REMARK 280 FORMATE, VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 293K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 21 21 21 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X+1/2,-Y,Z+1/2 REMARK 290 3555 -X,Y+1/2,-Z+1/2 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 18.29950 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 26.90300 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 24.58450 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 26.90300 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 18.29950 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 24.58450 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 GLY A 637 REMARK 465 ALA A 638 REMARK 465 MET A 639 REMARK 465 ALA A 640 REMARK 465 ASN A 641 REMARK 465 THR A 642 REMARK 465 GLN A 643 REMARK 465 SER A 644 REMARK 470 REMARK 470 MISSING ATOM REMARK 470 THE FOLLOWING RESIDUES HAVE MISSING ATOMS (M=MODEL NUMBER; REMARK 470 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; REMARK 470 I=INSERTION CODE): REMARK 470 M RES CSSEQI ATOMS REMARK 470 GLU A 645 CG CD OE1 OE2 REMARK 470 HIS A 646 CG ND1 CD2 CE1 NE2 REMARK 470 LYS A 684 CG CD CE NZ REMARK 470 GLU A 709 CD OE1 OE2 REMARK 470 LYS A 728 CE NZ REMARK 470 GLN A 739 CB CG CD OE1 NE2 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 OD2 ASP A 716 O HOH A 852 1.99 REMARK 500 OE1 GLU A 702 O HOH A 885 2.15 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 HIS A 738 32.75 -99.47 REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 4QAZ RELATED DB: PDB DBREF 4QB0 A 641 739 UNP P18272 NCAP_EBOZM 641 739 SEQADV 4QB0 GLY A 637 UNP P18272 EXPRESSION TAG SEQADV 4QB0 ALA A 638 UNP P18272 EXPRESSION TAG SEQADV 4QB0 MET A 639 UNP P18272 EXPRESSION TAG SEQADV 4QB0 ALA A 640 UNP P18272 EXPRESSION TAG SEQRES 1 A 103 GLY ALA MET ALA ASN THR GLN SER GLU HIS SER PHE GLU SEQRES 2 A 103 GLU MET TYR ARG HIS ILE LEU ARG SER GLN GLY PRO PHE SEQRES 3 A 103 ASP ALA VAL LEU TYR TYR HIS MET MET LYS ASP GLU PRO SEQRES 4 A 103 VAL VAL PHE SER THR SER ASP GLY LYS GLU TYR THR TYR SEQRES 5 A 103 PRO ASP SER LEU GLU GLU GLU TYR PRO PRO TRP LEU THR SEQRES 6 A 103 GLU LYS GLU ALA MET ASN GLU GLU ASN ARG PHE VAL THR SEQRES 7 A 103 LEU ASP GLY GLN GLN PHE TYR TRP PRO VAL MET ASN HIS SEQRES 8 A 103 LYS ASN LYS PHE MET ALA ILE LEU GLN HIS HIS GLN FORMUL 2 HOH *95(H2 O) HELIX 1 1 GLU A 645 GLY A 660 1 16 HELIX 2 2 GLY A 660 ASP A 673 1 14 HELIX 3 3 PRO A 689 GLU A 693 5 5 HELIX 4 4 THR A 701 ASN A 707 1 7 HELIX 5 5 GLU A 708 ASN A 710 5 3 HELIX 6 6 PRO A 723 MET A 725 5 3 HELIX 7 7 ASN A 726 HIS A 738 1 13 SHEET 1 A 2 VAL A 676 SER A 679 0 SHEET 2 A 2 GLU A 685 TYR A 688 -1 O TYR A 688 N VAL A 676 SHEET 1 B 2 PHE A 712 LEU A 715 0 SHEET 2 B 2 GLN A 718 TYR A 721 -1 O PHE A 720 N VAL A 713 CISPEP 1 TYR A 688 PRO A 689 0 2.80 CRYST1 36.599 49.169 53.806 90.00 90.00 90.00 P 21 21 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 0.027323 0.000000 0.000000 0.00000 SCALE2 0.000000 0.020338 0.000000 0.00000 SCALE3 0.000000 0.000000 0.018585 0.00000