HEADER CELL ADHESION 02-MAR-17 5V23 TITLE SEMET CRYSTAL STRUCTURE OF THE NEISSERIA MENINGITIDIS NON-CORE MINOR TITLE 2 PILIN PILV IN THE ORTHORHOMBIC 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 4 16-OCT-24 5V23 1 REMARK REVDAT 3 08-JAN-20 5V23 1 REMARK REVDAT 2 28-FEB-18 5V23 1 TITLE REVDAT 1 07-FEB-18 5V23 0 JRNL AUTH S.KOLAPPAN,L.CRAIG JRNL TITL SEMET STRUCTURE OF THE NON-CORE MINOR PILIN PILV FROM JRNL TITL 2 NEISSERIA MENINGITIDIS IN THE ORTHORHOMBIC FORM JRNL REF TO BE PUBLISHED JRNL REFN REMARK 2 REMARK 2 RESOLUTION. 1.96 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) : 1.96 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 37.03 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.360 REMARK 3 COMPLETENESS FOR RANGE (%) : 98.5 REMARK 3 NUMBER OF REFLECTIONS : 7217 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.188 REMARK 3 R VALUE (WORKING SET) : 0.185 REMARK 3 FREE R VALUE : 0.255 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.140 REMARK 3 FREE R VALUE TEST SET COUNT : 371 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 37.0365 - 2.8201 1.00 2392 138 0.1775 0.2374 REMARK 3 2 2.8201 - 2.2385 0.99 2273 125 0.2028 0.2888 REMARK 3 3 2.2385 - 1.9556 0.97 2181 108 0.1805 0.2656 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) : 0.100 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 25.240 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 : 0.007 824 REMARK 3 ANGLE : 0.932 1111 REMARK 3 CHIRALITY : 0.048 120 REMARK 3 PLANARITY : 0.005 146 REMARK 3 DIHEDRAL : 16.705 502 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : 1 REMARK 3 TLS GROUP : 1 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 25 THROUGH 122 ) REMARK 3 ORIGIN FOR THE GROUP (A): 13.3261 15.2013 70.6041 REMARK 3 T TENSOR REMARK 3 T11: 0.1712 T22: 0.1332 REMARK 3 T33: 0.1255 T12: 0.0098 REMARK 3 T13: 0.0354 T23: 0.0162 REMARK 3 L TENSOR REMARK 3 L11: 0.6047 L22: 2.1784 REMARK 3 L33: 0.8871 L12: 0.5350 REMARK 3 L13: -0.2072 L23: -0.5477 REMARK 3 S TENSOR REMARK 3 S11: -0.0482 S12: 0.0340 S13: -0.0789 REMARK 3 S21: -0.4822 S22: -0.0018 S23: -0.1802 REMARK 3 S31: -0.0291 S32: -0.0256 S33: 0.0009 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 5V23 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 22-MAR-17. REMARK 100 THE DEPOSITION ID IS D_1000226765. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 29-JAN-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 : BL7-1 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.976047, 0.979412 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 315R REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : AIMLESS REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 7263 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.956 REMARK 200 RESOLUTION RANGE LOW (A) : 54.810 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 98.7 REMARK 200 DATA REDUNDANCY : 7.300 REMARK 200 R MERGE (I) : 0.06600 REMARK 200 R SYM (I) : NULL REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 23.9000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.96 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.00 REMARK 200 COMPLETENESS FOR SHELL (%) : 89.2 REMARK 200 DATA REDUNDANCY IN SHELL : 5.70 REMARK 200 R MERGE FOR SHELL (I) : 0.28800 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 <I/SIGMA(I)> FOR SHELL : 5.500 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: MAD REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MAD REMARK 200 SOFTWARE USED: SOLVE REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 42.01 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.12 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: PEG 8000, AMMONIUM CHLORIDE, SODIUM REMARK 280 ACETATE PH 5.0, VAPOR DIFFUSION, HANGING 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 10.89700 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 54.80500 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 19.67150 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 54.80500 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 10.89700 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 19.67150 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: 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 LYS A 58 O HOH A 301 2.06 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 NH2 ARG A 52 O HOH A 301 1655 2.16 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 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue GOL A 202 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue GOL A 203 DBREF1 5V23 A 29 122 UNP A0A1B1ZB31_NEIME DBREF2 5V23 A A0A1B1ZB31 36 129 SEQADV 5V23 GLY A 25 UNP A0A1B1ZB3 EXPRESSION TAG SEQADV 5V23 SER A 26 UNP A0A1B1ZB3 EXPRESSION TAG SEQADV 5V23 HIS A 27 UNP A0A1B1ZB3 EXPRESSION TAG SEQADV 5V23 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 5V23 MSE A 47 MET MODIFIED RESIDUE HET MSE A 28 8 HET MSE A 47 16 HET GOL A 201 6 HET GOL A 202 6 HET GOL A 203 6 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 3(C3 H8 O3) FORMUL 5 HOH *73(H2 O) HELIX 1 AA1 GLY A 25 GLY A 55 1 31 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 ASP A 88 N ASN A 72 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 2.05 LINK C HIS A 27 N MSE A 28 1555 1555 1.33 LINK C MSE A 28 N ARG A 29 1555 1555 1.34 LINK C THR A 46 N AMSE A 47 1555 1555 1.33 LINK C THR A 46 N BMSE A 47 1555 1555 1.33 LINK C AMSE A 47 N GLU A 48 1555 1555 1.34 LINK C BMSE A 47 N GLU A 48 1555 1555 1.34 SITE 1 AC1 7 GLY A 25 MSE A 28 ASP A 95 VAL A 100 SITE 2 AC1 7 THR A 102 SER A 112 HOH A 306 SITE 1 AC2 5 THR A 102 ASN A 104 THR A 108 HOH A 307 SITE 2 AC2 5 HOH A 348 SITE 1 AC3 5 MSE A 28 ARG A 32 TYR A 70 THR A 114 SITE 2 AC3 5 HOH A 308 CRYST1 21.794 39.343 109.610 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 0.045884 0.000000 0.000000 0.00000 SCALE2 0.000000 0.025417 0.000000 0.00000 SCALE3 0.000000 0.000000 0.009123 0.00000