HEADER VIRAL PROTEIN 17-DEC-18 6Q99 TITLE ANDE VIRUS L PROTEIN N-TERMINUS MUTANT K124A COMPND MOL_ID: 1; COMPND 2 MOLECULE: RNA POLYMERASE; COMPND 3 CHAIN: A; COMPND 4 ENGINEERED: YES; COMPND 5 MUTATION: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: ANDES ORTHOHANTAVIRUS; SOURCE 3 ORGANISM_TAXID: 1980456; SOURCE 4 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 5 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS ANDES VIRUS, NUCLEASE, L PROTEIN, CAP-SNATCHING, VIRAL PROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR Y.FERNANDEZ-GARCIA,T.HOLM,J.KIRCHMAIR,S.WURR,S.GUNTHER,S.REINDL REVDAT 2 24-JAN-24 6Q99 1 LINK REVDAT 1 15-JAN-20 6Q99 0 SPRSDE 15-JAN-20 6Q99 5HSB JRNL AUTH Y.FERNANDEZ-GARCIA,J.KIRCHMAIR,T.HOLM,S.WURR,S.GUNTHER, JRNL AUTH 2 S.REINDL JRNL TITL SPECIFIC INHIBITION OF A DIVERSE SET OF SEGMENTED NEGATIVE JRNL TITL 2 STRAND VIRUSES BY A SINGLE MOLECULE JRNL REF TO BE PUBLISHED JRNL REFN REMARK 2 REMARK 2 RESOLUTION. 2.95 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.9_1692 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 : NULL REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.95 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 79.60 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.510 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.9 REMARK 3 NUMBER OF REFLECTIONS : 6153 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.246 REMARK 3 R VALUE (WORKING SET) : 0.238 REMARK 3 FREE R VALUE : 0.313 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 9.930 REMARK 3 FREE R VALUE TEST SET COUNT : 611 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 79.6278 - 4.6843 1.00 1471 164 0.2183 0.2966 REMARK 3 2 4.6843 - 3.7181 1.00 1373 152 0.2085 0.2569 REMARK 3 3 3.7181 - 3.2481 1.00 1362 150 0.2667 0.3644 REMARK 3 4 3.2481 - 2.9511 1.00 1336 145 0.2885 0.3768 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : NULL 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) : 0.520 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 30.920 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 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 1647 REMARK 3 ANGLE : 1.312 2225 REMARK 3 CHIRALITY : 0.060 249 REMARK 3 PLANARITY : 0.007 289 REMARK 3 DIHEDRAL : 17.912 635 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : 1 REMARK 3 TLS GROUP : 1 REMARK 3 SELECTION: ALL REMARK 3 ORIGIN FOR THE GROUP (A): 176.8885 149.4285 95.4819 REMARK 3 T TENSOR REMARK 3 T11: 0.1671 T22: 0.1977 REMARK 3 T33: 0.3516 T12: -0.0819 REMARK 3 T13: 0.0436 T23: 0.0010 REMARK 3 L TENSOR REMARK 3 L11: 0.9728 L22: 1.3196 REMARK 3 L33: 0.9511 L12: 0.0188 REMARK 3 L13: 0.4539 L23: -0.3636 REMARK 3 S TENSOR REMARK 3 S11: 0.0627 S12: -0.3926 S13: 0.1764 REMARK 3 S21: -0.0227 S22: -0.0070 S23: 0.2317 REMARK 3 S31: -0.0222 S32: -0.1824 S33: -0.0415 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 6Q99 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 18-DEC-18. REMARK 100 THE DEPOSITION ID IS D_1200012338. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 18-SEP-17 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 : PETRA III, EMBL C/O DESY REMARK 200 BEAMLINE : P13 (MX1) 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 : MOSFLM REMARK 200 DATA SCALING SOFTWARE : AIMLESS REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 6154 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.951 REMARK 200 RESOLUTION RANGE LOW (A) : 79.600 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 100.0 REMARK 200 DATA REDUNDANCY : 2.000 REMARK 200 R MERGE (I) : 0.05054 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 9.2000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.95 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 3.06 REMARK 200 COMPLETENESS FOR SHELL (%) : 100.0 REMARK 200 DATA REDUNDANCY IN SHELL : 2.00 REMARK 200 R MERGE FOR SHELL (I) : 0.12090 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 4.770 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: 5HSB REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 57.89 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.92 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 400MM (NH4)2SO4, 27% PEG3350, 100MM REMARK 280 NAAC PH5.5, 10MM MNCL2, VAPOR DIFFUSION, SITTING DROP, REMARK 280 TEMPERATURE 295K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 4 21 2 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 -Y+1/2,X+1/2,Z REMARK 290 4555 Y+1/2,-X+1/2,Z REMARK 290 5555 -X+1/2,Y+1/2,-Z REMARK 290 6555 X+1/2,-Y+1/2,-Z REMARK 290 7555 Y,X,-Z REMARK 290 8555 -Y,-X,-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 0.00000 REMARK 290 SMTRY1 3 0.000000 -1.000000 0.000000 41.17050 REMARK 290 SMTRY2 3 1.000000 0.000000 0.000000 41.17050 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 4 0.000000 1.000000 0.000000 41.17050 REMARK 290 SMTRY2 4 -1.000000 0.000000 0.000000 41.17050 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 5 -1.000000 0.000000 0.000000 41.17050 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 41.17050 REMARK 290 SMTRY3 5 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 6 1.000000 0.000000 0.000000 41.17050 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 41.17050 REMARK 290 SMTRY3 6 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 7 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY2 7 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 8 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY2 8 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 8 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 TOTAL BURIED SURFACE AREA: 530 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 11200 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -12.0 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 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 LYS A 200 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 ILE A 7 -61.32 -91.51 REMARK 500 GLN A 9 -70.91 -48.01 REMARK 500 VAL A 11 -61.05 -90.98 REMARK 500 SER A 20 -142.02 56.25 REMARK 500 HIS A 45 -60.19 -101.04 REMARK 500 TRP A 47 -65.23 -134.93 REMARK 500 ASP A 52 -76.40 -86.02 REMARK 500 LYS A 77 -169.68 -75.49 REMARK 500 LEU A 198 -71.69 -107.07 REMARK 500 REMARK 500 REMARK: NULL REMARK 620 REMARK 620 METAL COORDINATION REMARK 620 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 620 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE): REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MN3 A 302 MN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 GLU A 54 OE1 REMARK 620 2 ASP A 97 OD1 88.0 REMARK 620 N 1 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MN3 A 301 MN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP A 97 OD2 REMARK 620 2 VAL A 111 O 85.0 REMARK 620 N 1 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue MN3 A 301 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue MN3 A 302 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue GOL A 303 DBREF 6Q99 A 1 200 UNP Q9E005 Q9E005_9VIRU 1 200 SEQADV 6Q99 GLY A -1 UNP Q9E005 EXPRESSION TAG SEQADV 6Q99 PRO A 0 UNP Q9E005 EXPRESSION TAG SEQADV 6Q99 ALA A 124 UNP Q9E005 LYS 124 ENGINEERED MUTATION SEQADV 6Q99 ILE A 181 UNP Q9E005 VAL 181 CONFLICT SEQRES 1 A 202 GLY PRO MET GLU LYS TYR ARG GLU ILE HIS GLN ARG VAL SEQRES 2 A 202 ARG ASP LEU ALA PRO GLY THR VAL SER ALA LEU GLU CYS SEQRES 3 A 202 ILE ASP LEU LEU ASP ARG LEU TYR ALA VAL ARG HIS ASP SEQRES 4 A 202 LEU VAL ASP GLN MET ILE LYS HIS ASP TRP SER ASP ASN SEQRES 5 A 202 LYS ASP VAL GLU ARG PRO ILE GLY GLN VAL LEU LEU MET SEQRES 6 A 202 ALA GLY ILE PRO ASN ASP ILE ILE GLN GLY MET GLU LYS SEQRES 7 A 202 LYS ILE ILE PRO ASN SER PRO SER GLY GLN VAL LEU LYS SEQRES 8 A 202 SER PHE PHE ARG MET THR PRO ASP ASN TYR LYS ILE THR SEQRES 9 A 202 GLY ASN LEU ILE GLU PHE ILE GLU VAL THR VAL THR ALA SEQRES 10 A 202 ASP VAL SER ARG GLY ILE ARG GLU ALA LYS ILE LYS TYR SEQRES 11 A 202 GLU GLY GLY LEU GLN PHE VAL GLU HIS LEU LEU GLU THR SEQRES 12 A 202 GLU SER ARG LYS GLY ASN ILE PRO GLN PRO TYR LYS ILE SEQRES 13 A 202 THR PHE SER VAL VAL ALA VAL LYS THR ASP GLY SER ASN SEQRES 14 A 202 ILE SER THR GLN TRP PRO SER ARG ARG ASN ASP GLY VAL SEQRES 15 A 202 ILE GLN HIS MET ARG LEU VAL GLN ALA ASP ILE ASN TYR SEQRES 16 A 202 VAL ARG GLU HIS LEU ILE LYS HET MN3 A 301 1 HET MN3 A 302 1 HET GOL A 303 6 HETNAM MN3 MANGANESE (III) ION HETNAM GOL GLYCEROL HETSYN GOL GLYCERIN; PROPANE-1,2,3-TRIOL FORMUL 2 MN3 2(MN 3+) FORMUL 4 GOL C3 H8 O3 FORMUL 5 HOH *5(H2 O) HELIX 1 AA1 PRO A 0 ASP A 13 1 14 HELIX 2 AA2 GLU A 23 TRP A 47 1 25 HELIX 3 AA3 PRO A 56 ALA A 64 1 9 HELIX 4 AA4 PRO A 67 GLN A 72 1 6 HELIX 5 AA5 GLY A 73 LYS A 77 5 5 HELIX 6 AA6 VAL A 87 PHE A 92 1 6 HELIX 7 AA7 ASP A 116 TYR A 128 1 13 HELIX 8 AA8 TYR A 128 ARG A 144 1 17 HELIX 9 AA9 ASN A 167 TRP A 172 1 6 HELIX 10 AB1 ARG A 176 GLU A 196 1 21 SHEET 1 AA1 3 ASN A 98 THR A 102 0 SHEET 2 AA1 3 LEU A 105 THR A 112 -1 O GLU A 107 N LYS A 100 SHEET 3 AA1 3 LYS A 153 ALA A 160 1 O THR A 155 N PHE A 108 LINK OE1 GLU A 54 MN MN3 A 302 1555 1555 2.55 LINK OD2 ASP A 97 MN MN3 A 301 1555 1555 2.52 LINK OD1 ASP A 97 MN MN3 A 302 1555 1555 2.36 LINK O VAL A 111 MN MN3 A 301 1555 1555 2.53 SITE 1 AC1 4 HIS A 36 ASP A 97 GLU A 110 VAL A 111 SITE 1 AC2 3 GLU A 54 THR A 95 ASP A 97 SITE 1 AC3 5 ARG A 35 VAL A 113 THR A 114 ALA A 115 SITE 2 AC3 5 ARG A 195 CRYST1 82.341 82.341 79.599 90.00 90.00 90.00 P 4 21 2 8 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 0.012145 0.000000 0.000000 0.00000 SCALE2 0.000000 0.012145 0.000000 0.00000 SCALE3 0.000000 0.000000 0.012563 0.00000