HEADER VIRAL PROTEIN 06-MAY-14 4QAZ 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 4QAZ 1 SEQADV REVDAT 2 24-SEP-14 4QAZ 1 JRNL REVDAT 1 10-SEP-14 4QAZ 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. 1.98 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) : 1.98 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 26.65 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.150 REMARK 3 COMPLETENESS FOR RANGE (%) : 96.0 REMARK 3 NUMBER OF REFLECTIONS : 8427 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.186 REMARK 3 R VALUE (WORKING SET) : 0.184 REMARK 3 FREE R VALUE : 0.229 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.710 REMARK 3 FREE R VALUE TEST SET COUNT : 729 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 26.6523 - 3.3621 0.99 3059 134 0.1699 0.2209 REMARK 3 2 3.3621 - 2.6694 1.00 3061 148 0.1981 0.2263 REMARK 3 3 2.6694 - 2.3322 1.00 3068 162 0.1974 0.2505 REMARK 3 4 2.3322 - 2.1190 1.00 3063 149 0.1993 0.2306 REMARK 3 5 2.1190 - 1.9672 0.82 2508 136 0.2155 0.2593 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) : 0.170 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 24.480 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 41.50 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 : 0.012 830 REMARK 3 ANGLE : 1.300 1127 REMARK 3 CHIRALITY : 0.058 111 REMARK 3 PLANARITY : 0.007 146 REMARK 3 DIHEDRAL : 14.593 308 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 693 ) REMARK 3 ORIGIN FOR THE GROUP (A): 14.6465 0.3505 0.2454 REMARK 3 T TENSOR REMARK 3 T11: 0.2957 T22: 0.3816 REMARK 3 T33: 0.3241 T12: 0.0568 REMARK 3 T13: 0.0455 T23: -0.0728 REMARK 3 L TENSOR REMARK 3 L11: 2.2011 L22: 7.1608 REMARK 3 L33: 2.1633 L12: 1.6404 REMARK 3 L13: 0.0454 L23: -1.6300 REMARK 3 S TENSOR REMARK 3 S11: 0.0469 S12: -0.2182 S13: 0.2645 REMARK 3 S21: 0.5740 S22: -0.1089 S23: 0.6444 REMARK 3 S31: -0.3056 S32: -0.5095 S33: 0.0153 REMARK 3 TLS GROUP : 2 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 694 THROUGH 739 ) REMARK 3 ORIGIN FOR THE GROUP (A): 13.0003 -18.4598 -4.1656 REMARK 3 T TENSOR REMARK 3 T11: 0.2895 T22: 0.4089 REMARK 3 T33: 0.3131 T12: -0.0441 REMARK 3 T13: -0.0114 T23: 0.0070 REMARK 3 L TENSOR REMARK 3 L11: 2.8278 L22: 7.4847 REMARK 3 L33: 2.5851 L12: 0.9339 REMARK 3 L13: 0.6055 L23: -0.8894 REMARK 3 S TENSOR REMARK 3 S11: -0.1145 S12: -0.1534 S13: -0.0611 REMARK 3 S21: -0.2368 S22: 0.2649 S23: 0.5959 REMARK 3 S31: 0.3263 S32: -0.3242 S33: -0.1051 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 4QAZ 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_1000085826. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 06-DEC-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-ID REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.97907 REMARK 200 MONOCHROMATOR : SI(111) REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : MARMOSAIC 300 MM CCD REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 8428 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.980 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 (%) : 97.2 REMARK 200 DATA REDUNDANCY : 8.700 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : 0.12500 REMARK 200 FOR THE DATA SET : 12.5000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.98 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.01 REMARK 200 COMPLETENESS FOR SHELL (%) : 76.3 REMARK 200 DATA REDUNDANCY IN SHELL : 3.30 REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : 0.26200 REMARK 200 FOR SHELL : 3.700 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: SAD REMARK 200 SOFTWARE USED: SHELXE REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 48.19 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.37 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 19.3% PEG3350, 0.3M MAGNESIUM FORMATE, REMARK 280 VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 293K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 31 2 1 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 Y,X,-Z REMARK 290 5555 X-Y,-Y,-Z+2/3 REMARK 290 6555 -X,-X+Y,-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 21.18200 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 42.36400 REMARK 290 SMTRY1 4 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 4 0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 4 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 5 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 5 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 5 0.000000 0.000000 -1.000000 42.36400 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 21.18200 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 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 836 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 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 GLU A 695 CG CD OE1 OE2 REMARK 470 GLU A 702 CD OE1 OE2 REMARK 470 MET A 706 SD CE REMARK 470 GLU A 708 CG CD OE1 OE2 REMARK 470 GLU A 709 CD OE1 OE2 REMARK 470 GLN A 739 O 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 O HOH A 846 O HOH A 861 1.83 REMARK 500 O HOH A 858 O HOH A 890 1.96 REMARK 500 O HOH A 835 O HOH A 872 1.98 REMARK 500 O HOH A 860 O HOH A 867 2.01 REMARK 500 O HOH A 819 O HOH A 864 2.04 REMARK 500 OXT GLN A 739 O HOH A 892 2.06 REMARK 500 O HOH A 811 O HOH A 880 2.07 REMARK 500 O HOH A 835 O HOH A 875 2.08 REMARK 500 O HOH A 833 O HOH A 841 2.10 REMARK 500 O HOH A 891 O HOH A 893 2.11 REMARK 500 O HOH A 877 O HOH A 887 2.11 REMARK 500 OH TYR A 721 O HOH A 867 2.13 REMARK 500 O HOH A 842 O HOH A 852 2.16 REMARK 500 O HOH A 868 O HOH A 900 2.18 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 O HOH A 889 O HOH A 894 4545 1.95 REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 4QB0 RELATED DB: PDB DBREF 4QAZ A 641 739 UNP P18272 NCAP_EBOZM 641 739 SEQADV 4QAZ GLY A 637 UNP P18272 EXPRESSION TAG SEQADV 4QAZ ALA A 638 UNP P18272 EXPRESSION TAG SEQADV 4QAZ MET A 639 UNP P18272 EXPRESSION TAG SEQADV 4QAZ 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 *100(H2 O) HELIX 1 1 GLU A 645 GLN A 659 1 15 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 LYS A 703 ASN A 710 5 8 HELIX 5 5 PRO A 723 MET A 725 5 3 HELIX 6 6 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 686 N PHE A 678 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 5.84 CRYST1 56.515 56.515 63.546 90.00 90.00 120.00 P 31 2 1 6 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 0.017694 0.010216 0.000000 0.00000 SCALE2 0.000000 0.020432 0.000000 0.00000 SCALE3 0.000000 0.000000 0.015737 0.00000