HEADER VIRAL PROTEIN 09-OCT-16 5M1M TITLE CRYSTAL STRUCTURE OF MATRIX PROTEIN 1 FROM INFLUENZA C VIRUS (STRAIN TITLE 2 C/ANN ARBOR/1/1950) COMPND MOL_ID: 1; COMPND 2 MOLECULE: MATRIX PROTEIN 1; COMPND 3 CHAIN: A; COMPND 4 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: INFLUENZA C VIRUS (STRAIN C/ANN ARBOR/1/1950); SOURCE 3 ORGANISM_TAXID: 11553; SOURCE 4 STRAIN: C/ANN ARBOR/1/1950; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 6 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS INFLUENZA C, MATRIX PROTEIN 1, VIRAL PROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR J.RADZIMANOWSKI,W.WEISSENHORN REVDAT 2 06-SEP-17 5M1M 1 REMARK REVDAT 1 08-FEB-17 5M1M 0 JRNL AUTH D.SALETTI,J.RADZIMANOWSKI,G.EFFANTIN,D.MIDTVEDT,S.MANGENOT, JRNL AUTH 2 W.WEISSENHORN,P.BASSEREAU,M.BALLY JRNL TITL THE MATRIX PROTEIN M1 FROM INFLUENZA C VIRUS INDUCES TUBULAR JRNL TITL 2 MEMBRANE INVAGINATIONS IN AN IN VITRO CELL MEMBRANE MODEL. JRNL REF SCI REP V. 7 40801 2017 JRNL REFN ESSN 2045-2322 JRNL PMID 28120862 JRNL DOI 10.1038/SREP40801 REMARK 2 REMARK 2 RESOLUTION. 1.50 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.8_1069 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) : 1.50 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 31.50 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.350 REMARK 3 COMPLETENESS FOR RANGE (%) : 98.9 REMARK 3 NUMBER OF REFLECTIONS : 20868 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.189 REMARK 3 R VALUE (WORKING SET) : 0.188 REMARK 3 FREE R VALUE : 0.220 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.150 REMARK 3 FREE R VALUE TEST SET COUNT : 1074 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 31.5089 - 2.9993 0.98 2540 141 0.1795 0.1992 REMARK 3 2 2.9993 - 2.3809 0.99 2498 133 0.1879 0.2012 REMARK 3 3 2.3809 - 2.0800 0.99 2491 123 0.1731 0.2090 REMARK 3 4 2.0800 - 1.8898 0.99 2459 139 0.1896 0.2468 REMARK 3 5 1.8898 - 1.7544 0.99 2490 131 0.1998 0.2556 REMARK 3 6 1.7544 - 1.6510 1.00 2458 147 0.2102 0.2789 REMARK 3 7 1.6510 - 1.5683 0.99 2418 126 0.2096 0.2620 REMARK 3 8 1.5683 - 1.5000 0.99 2440 134 0.2250 0.2364 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) : 0.120 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 22.420 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 : 0.006 1195 REMARK 3 ANGLE : 0.969 1601 REMARK 3 CHIRALITY : 0.068 180 REMARK 3 PLANARITY : 0.005 200 REMARK 3 DIHEDRAL : 12.511 468 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : NULL 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 5M1M COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 10-OCT-16. REMARK 100 THE DEPOSITION ID IS D_1200001735. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 12-NOV-12 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 8.0 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : ESRF REMARK 200 BEAMLINE : ID29 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.93928 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS PILATUS 6M-F REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : SCALA REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 20888 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.500 REMARK 200 RESOLUTION RANGE LOW (A) : 36.640 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.2 REMARK 200 DATA REDUNDANCY : 3.700 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : 0.06300 REMARK 200 FOR THE DATA SET : 12.1000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.50 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.58 REMARK 200 COMPLETENESS FOR SHELL (%) : 99.3 REMARK 200 DATA REDUNDANCY IN SHELL : 3.80 REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : 0.52700 REMARK 200 FOR SHELL : 2.400 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: SAD 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 (%): 34.15 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 1.87 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 100MM TRIS PH8.0, 200MM MGCL2 AND25% REMARK 280 PEG3350, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 293K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: C 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 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 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 33.19900 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 13.42050 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 4 -1.000000 0.000000 0.000000 33.19900 REMARK 290 SMTRY2 4 0.000000 1.000000 0.000000 13.42050 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 SOFTWARE DETERMINED QUATERNARY STRUCTURE: MONOMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 200 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 8130 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -17.0 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 MET A 1 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 365 O HOH A 411 2.06 REMARK 500 O HOH A 433 O HOH A 435 2.13 REMARK 500 O HOH A 353 O HOH A 399 2.15 REMARK 500 NH2 ARG A 114 O HOH A 301 2.17 REMARK 500 O SER A 155 O HOH A 302 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 348 O HOH A 435 4556 2.02 REMARK 500 O HOH A 384 O HOH A 411 4555 2.09 REMARK 500 O HOH A 327 O HOH A 415 1565 2.12 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: COVALENT BOND LENGTHS REMARK 500 REMARK 500 THE STEREOCHEMICAL PARAMETERS OF THE FOLLOWING RESIDUES REMARK 500 HAVE VALUES WHICH DEVIATE FROM EXPECTED VALUES BY MORE REMARK 500 THAN 6*RMSD (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 500 IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 STANDARD TABLE: REMARK 500 FORMAT: (10X,I3,1X,2(A3,1X,A1,I4,A1,1X,A4,3X),1X,F6.3) REMARK 500 REMARK 500 EXPECTED VALUES PROTEIN: ENGH AND HUBER, 1999 REMARK 500 EXPECTED VALUES NUCLEIC ACID: CLOWNEY ET AL 1996 REMARK 500 REMARK 500 M RES CSSEQI ATM1 RES CSSEQI ATM2 DEVIATION REMARK 500 GLU A 4 CD GLU A 4 OE2 -0.080 REMARK 500 GLU A 46 CD GLU A 46 OE1 -0.072 REMARK 500 GLU A 46 CD GLU A 46 OE2 -0.104 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 MG A 201 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASN A 80 OD1 REMARK 620 2 GLU A 126 OE2 84.9 REMARK 620 3 ASP A 130 OD2 174.2 93.9 REMARK 620 4 HOH A 326 O 88.7 97.3 85.8 REMARK 620 5 HOH A 386 O 92.6 89.0 93.0 173.7 REMARK 620 6 HOH A 390 O 95.0 176.0 86.6 86.7 87.0 REMARK 620 N 1 2 3 4 5 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MG A 202 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 THR A 83 OG1 REMARK 620 2 GLU A 123 OE1 91.3 REMARK 620 3 GLU A 126 OE1 87.6 85.3 REMARK 620 4 HOH A 316 O 88.0 171.9 86.7 REMARK 620 5 HOH A 324 O 84.8 93.3 172.2 94.7 REMARK 620 6 HOH A 329 O 174.9 90.7 97.2 90.6 90.4 REMARK 620 N 1 2 3 4 5 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue MG A 201 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue MG A 202 DBREF 5M1M A 1 155 UNP Q6I7B9 MAT_INCAA 1 155 SEQRES 1 A 155 MET ALA HIS GLU ILE LEU ILE ALA GLU THR GLU ALA PHE SEQRES 2 A 155 LEU LYS ASN VAL ALA PRO GLU THR ARG THR ALA ILE ILE SEQRES 3 A 155 SER ALA ILE THR GLY GLY LYS SER ALA CYS LYS SER ALA SEQRES 4 A 155 ALA LYS LEU ILE LYS ASN GLU HIS LEU PRO LEU MET SER SEQRES 5 A 155 GLY GLU ALA THR THR MET HIS ILE VAL MET ARG CYS LEU SEQRES 6 A 155 TYR PRO GLU ILE LYS PRO TRP LYS LYS ALA SER ASP MET SEQRES 7 A 155 LEU ASN LYS ALA THR SER SER LEU LYS LYS SER GLU GLY SEQRES 8 A 155 ARG ASP ILE ARG LYS GLN MET LYS ALA ALA GLY ASP PHE SEQRES 9 A 155 LEU GLY VAL GLU SER MET MET LYS MET ARG ALA PHE ARG SEQRES 10 A 155 ASP ASP GLN ILE MET GLU MET VAL GLU GLU VAL TYR ASP SEQRES 11 A 155 HIS PRO ASP ASP TYR THR PRO ASP ILE ARG ILE GLY THR SEQRES 12 A 155 ILE THR ALA TRP LEU ARG CYS LYS ASN LYS LYS SER HET MG A 201 1 HET MG A 202 1 HETNAM MG MAGNESIUM ION FORMUL 2 MG 2(MG 2+) FORMUL 4 HOH *169(H2 O) HELIX 1 AA1 ALA A 2 LEU A 14 1 13 HELIX 2 AA2 ALA A 18 THR A 30 1 13 HELIX 3 AA3 GLY A 32 ASN A 45 1 14 HELIX 4 AA4 MET A 51 TYR A 66 1 16 HELIX 5 AA5 TRP A 72 THR A 83 1 12 HELIX 6 AA6 LYS A 87 GLY A 102 1 16 HELIX 7 AA7 ASP A 103 ARG A 114 1 12 HELIX 8 AA8 ARG A 117 HIS A 131 1 15 HELIX 9 AA9 PRO A 132 TYR A 135 5 4 HELIX 10 AB1 THR A 136 LYS A 153 1 18 LINK OD1 ASN A 80 MG MG A 201 1555 1555 2.02 LINK OG1 THR A 83 MG MG A 202 1555 1555 2.20 LINK OE1 GLU A 123 MG MG A 202 1555 1555 2.19 LINK OE1 GLU A 126 MG MG A 202 1555 1555 2.03 LINK OE2 GLU A 126 MG MG A 201 1555 1555 2.07 LINK OD2 ASP A 130 MG MG A 201 1555 1555 2.05 LINK MG MG A 201 O HOH A 326 1555 1555 2.15 LINK MG MG A 201 O HOH A 386 1555 1555 2.03 LINK MG MG A 201 O HOH A 390 1555 1555 2.17 LINK MG MG A 202 O HOH A 316 1555 1555 2.07 LINK MG MG A 202 O HOH A 324 1555 1555 2.06 LINK MG MG A 202 O HOH A 329 1555 1555 2.09 SITE 1 AC1 6 ASN A 80 GLU A 126 ASP A 130 HOH A 326 SITE 2 AC1 6 HOH A 386 HOH A 390 SITE 1 AC2 6 THR A 83 GLU A 123 GLU A 126 HOH A 316 SITE 2 AC2 6 HOH A 324 HOH A 329 CRYST1 66.398 26.841 77.224 90.00 108.40 90.00 C 1 2 1 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 0.015061 0.000000 0.005010 0.00000 SCALE2 0.000000 0.037256 0.000000 0.00000 SCALE3 0.000000 0.000000 0.013647 0.00000