HEADER CELL ADHESION 28-FEB-17 5V0M TITLE SEMET CRYSTAL STRUCTURE OF THE NEISSERIA MENINGITIDIS NON-CORE MINOR TITLE 2 PILIN PILV IN THE MONOCLINIC FORM COMPND MOL_ID: 1; COMPND 2 MOLECULE: TYPE IV PILIN PROTEIN; COMPND 3 CHAIN: A; COMPND 4 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: NEISSERIA MENINGITIDIS; SOURCE 3 ORGANISM_TAXID: 487; SOURCE 4 GENE: A6L27_01160; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 6 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS PILIN, MINOR PILIN, TYPE IV PILI, NEISSERIA MENINGITIDIS, CELL KEYWDS 2 ADHESION EXPDTA X-RAY DIFFRACTION AUTHOR S.KOLAPPAN,L.CRAIG REVDAT 5 16-OCT-24 5V0M 1 REMARK REVDAT 4 15-NOV-23 5V0M 1 REMARK REVDAT 3 04-OCT-23 5V0M 1 REMARK REVDAT 2 08-JAN-20 5V0M 1 REMARK REVDAT 1 28-FEB-18 5V0M 0 JRNL AUTH S.KOLAPPAN,L.CRAIG JRNL TITL CRYSTAL STRUCTURE OF PILV FROM NEISSERIA MENINGITIDIS JRNL REF TO BE PUBLISHED JRNL REFN REMARK 2 REMARK 2 RESOLUTION. 1.41 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX (1.10.1_2155: ???) 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) : 1.41 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 27.08 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.330 REMARK 3 COMPLETENESS FOR RANGE (%) : 95.2 REMARK 3 NUMBER OF REFLECTIONS : 15402 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.174 REMARK 3 R VALUE (WORKING SET) : 0.172 REMARK 3 FREE R VALUE : 0.206 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.270 REMARK 3 FREE R VALUE TEST SET COUNT : 811 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 27.0894 - 2.5564 0.95 2502 144 0.1546 0.1781 REMARK 3 2 2.5564 - 2.0293 0.94 2427 144 0.1699 0.2073 REMARK 3 3 2.0293 - 1.7728 0.96 2424 142 0.1756 0.2059 REMARK 3 4 1.7728 - 1.6108 0.96 2427 135 0.1943 0.2563 REMARK 3 5 1.6108 - 1.4953 0.94 2382 106 0.2017 0.2536 REMARK 3 6 1.4953 - 1.4072 0.96 2429 140 0.2048 0.2556 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) : 0.140 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 22.610 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 : 0.009 860 REMARK 3 ANGLE : 1.024 1165 REMARK 3 CHIRALITY : 0.080 125 REMARK 3 PLANARITY : 0.006 156 REMARK 3 DIHEDRAL : 13.138 336 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 5V0M COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 08-MAR-17. REMARK 100 THE DEPOSITION ID IS D_1000226684. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 02-FEB-17 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : SSRL REMARK 200 BEAMLINE : BL12-2 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.96859 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS PILATUS 6M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : AIMLESS REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 15424 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.407 REMARK 200 RESOLUTION RANGE LOW (A) : 40.630 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 95.9 REMARK 200 DATA REDUNDANCY : 5.900 REMARK 200 R MERGE (I) : 0.09800 REMARK 200 R SYM (I) : NULL REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 12.2000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.41 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.43 REMARK 200 COMPLETENESS FOR SHELL (%) : 97.0 REMARK 200 DATA REDUNDANCY IN SHELL : 6.00 REMARK 200 R MERGE FOR SHELL (I) : 0.81900 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 <I/SIGMA(I)> FOR SHELL : 4.000 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: 5V23 REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 33.30 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 1.75 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 100 MM SODIUM ACETATE PH 5, 100 MM REMARK 280 AMMONIUM CHLORIDE, 28 % W/V PEG 8000, VAPOR DIFFUSION, HANGING REMARK 280 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 23.16000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 10.90000 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 4 -1.000000 0.000000 0.000000 23.16000 REMARK 290 SMTRY2 4 0.000000 1.000000 0.000000 10.90000 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 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 ASN A 115 70.13 21.13 REMARK 500 REMARK 500 REMARK: NULL REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue GOL A 201 DBREF1 5V0M A 29 122 UNP A0A1B1ZB31_NEIME DBREF2 5V0M A A0A1B1ZB31 36 129 SEQADV 5V0M GLY A 25 UNP A0A1B1ZB3 EXPRESSION TAG SEQADV 5V0M SER A 26 UNP A0A1B1ZB3 EXPRESSION TAG SEQADV 5V0M HIS A 27 UNP A0A1B1ZB3 EXPRESSION TAG SEQADV 5V0M MSE A 28 UNP A0A1B1ZB3 EXPRESSION TAG SEQRES 1 A 98 GLY SER HIS MSE ARG ARG VAL ARG LEU SER GLU VAL ARG SEQRES 2 A 98 THR THR LEU LEU HIS ASN ALA GLN THR MSE GLU ARG TYR SEQRES 3 A 98 TYR ARG GLN LYS GLY THR PHE LYS THR TYR ASP LYS ASN SEQRES 4 A 98 LYS LEU LYS GLN ASN LYS TYR PHE ASN VAL THR LEU SER SEQRES 5 A 98 LYS VAL SER PRO ASP HIS PHE THR LEU GLN ALA ASP PRO SEQRES 6 A 98 ASN PRO THR THR ASN ASP GLY GLU THR CYS VAL VAL THR SEQRES 7 A 98 LEU ASN ASP GLY GLY THR ILE ALA ALA SER GLY THR ASN SEQRES 8 A 98 GLN SER CYS PRO GLY PHE ASP MODRES 5V0M MSE A 47 MET MODIFIED RESIDUE HET MSE A 28 34 HET MSE A 47 34 HET GOL A 201 14 HETNAM MSE SELENOMETHIONINE HETNAM GOL GLYCEROL HETSYN GOL GLYCERIN; PROPANE-1,2,3-TRIOL FORMUL 1 MSE 2(C5 H11 N O2 SE) FORMUL 2 GOL C3 H8 O3 FORMUL 3 HOH *106(H2 O) HELIX 1 AA1 SER A 26 GLY A 55 1 30 HELIX 2 AA2 ASP A 61 LEU A 65 5 5 SHEET 1 AA1 4 PHE A 71 VAL A 78 0 SHEET 2 AA1 4 PHE A 83 PRO A 89 -1 O GLN A 86 N THR A 74 SHEET 3 AA1 4 VAL A 100 ASN A 104 -1 O LEU A 103 N LEU A 85 SHEET 4 AA1 4 ILE A 109 SER A 112 -1 O ALA A 110 N THR A 102 SSBOND 1 CYS A 99 CYS A 118 1555 1555 2.03 LINK C HIS A 27 N AMSE A 28 1555 1555 1.32 LINK C HIS A 27 N BMSE A 28 1555 1555 1.33 LINK C AMSE A 28 N ARG A 29 1555 1555 1.34 LINK C BMSE A 28 N ARG A 29 1555 1555 1.33 LINK C THR A 46 N AMSE A 47 1555 1555 1.32 LINK C THR A 46 N BMSE A 47 1555 1555 1.34 LINK C AMSE A 47 N AGLU A 48 1555 1555 1.33 LINK C BMSE A 47 N BGLU A 48 1555 1555 1.34 SITE 1 AC1 5 GLU A 48 PHE A 57 ASP A 81 ASP A 105 SITE 2 AC1 5 HOH A 311 CRYST1 46.320 21.800 83.830 90.00 104.24 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 0.021589 0.000000 0.005480 0.00000 SCALE2 0.000000 0.045871 0.000000 0.00000 SCALE3 0.000000 0.000000 0.012307 0.00000