HEADER CELL ADHESION 11-MAY-16 5JW8 TITLE CRYSTAL STRUCTURE OF THE TYPE IV PILIN SUBUNIT PILE FROM NEISSERIA TITLE 2 MENINGITIDIS COMPND MOL_ID: 1; COMPND 2 MOLECULE: MAJOR PILIN PILE; COMPND 3 CHAIN: A; COMPND 4 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: NEISSERIA MENINGITIDIS SEROGROUP C; SOURCE 3 ORGANISM_TAXID: 604162; SOURCE 4 STRAIN: 8013; SOURCE 5 GENE: PILE, NMV_0019; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS TYPE IV PILIN, CELL ADHESION EXPDTA X-RAY DIFFRACTION AUTHOR S.KOLAPPAN,L.CRAIG REVDAT 5 13-NOV-24 5JW8 1 REMARK REVDAT 4 27-SEP-23 5JW8 1 REMARK REVDAT 3 08-JAN-20 5JW8 1 REMARK REVDAT 2 26-OCT-16 5JW8 1 JRNL REVDAT 1 06-JUL-16 5JW8 0 SPRSDE 06-JUL-16 5JW8 4XNP JRNL AUTH S.KOLAPPAN,M.COUREUIL,X.YU,X.NASSIF,E.H.EGELMAN,L.CRAIG JRNL TITL STRUCTURE OF THE NEISSERIA MENINGITIDIS TYPE IV PILUS. JRNL REF NAT COMMUN V. 7 13015 2016 JRNL REFN ESSN 2041-1723 JRNL PMID 27698424 JRNL DOI 10.1038/NCOMMS13015 REMARK 2 REMARK 2 RESOLUTION. 1.44 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX (DEV_2299: ???) 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) : 1.44 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 33.43 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.360 REMARK 3 COMPLETENESS FOR RANGE (%) : 98.6 REMARK 3 NUMBER OF REFLECTIONS : 18030 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) : 0.187 REMARK 3 FREE R VALUE : 0.210 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.000 REMARK 3 FREE R VALUE TEST SET COUNT : 901 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 33.4408 - 2.6136 0.99 3017 159 0.1692 0.1794 REMARK 3 2 2.6136 - 2.0746 1.00 2908 153 0.1752 0.1966 REMARK 3 3 2.0746 - 1.8124 0.99 2838 150 0.1932 0.2293 REMARK 3 4 1.8124 - 1.6467 1.00 2879 151 0.1880 0.2221 REMARK 3 5 1.6467 - 1.5286 1.00 2842 150 0.2076 0.2079 REMARK 3 6 1.5286 - 1.4385 0.94 2645 138 0.2969 0.3986 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) : 0.170 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 23.570 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 : 0.004 1059 REMARK 3 ANGLE : 0.679 1450 REMARK 3 CHIRALITY : 0.068 168 REMARK 3 PLANARITY : 0.003 192 REMARK 3 DIHEDRAL : 12.143 386 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 5JW8 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 18-MAY-16. REMARK 100 THE DEPOSITION ID IS D_1000220167. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 13-DEC-14 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 6.0 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) : 0.9753 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 : XSCALE REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 18088 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.439 REMARK 200 RESOLUTION RANGE LOW (A) : 33.432 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 98.7 REMARK 200 DATA REDUNDANCY : 6.600 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 21.6000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : NULL REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : NULL REMARK 200 COMPLETENESS FOR SHELL (%) : NULL REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 <I/SIGMA(I)> FOR SHELL : NULL 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: MODIFIED 2HI2 REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 26.90 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 1.68 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 100 MM MES PH 6.0, 34 % (W/V) PEG4000, REMARK 280 100 MM AMMONIUM SULPHATE, VAPOR DIFFUSION, HANGING DROP, REMARK 280 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 21.72500 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 24.18500 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 23.13000 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 24.18500 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 21.72500 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 23.13000 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 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 GLY A 25 REMARK 465 SER A 26 REMARK 465 HIS A 27 REMARK 465 MET A 28 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 H ILE A 145 O HOH A 208 1.53 REMARK 500 HG1 THR A 141 O HOH A 204 1.59 REMARK 500 OE1 GLU A 35 O HOH A 201 1.87 REMARK 500 O HOH A 282 O HOH A 341 1.88 REMARK 500 O HOH A 307 O HOH A 353 1.91 REMARK 500 NH2 ARG A 111 O HOH A 202 2.06 REMARK 500 OG1 THR A 127 O HOH A 203 2.06 REMARK 500 OG1 THR A 141 O HOH A 204 2.09 REMARK 500 OG SER A 152 O HOH A 205 2.10 REMARK 500 NE2 GLN A 122 O ILE A 145 2.18 REMARK 500 O HOH A 319 O HOH A 325 2.19 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 218 O HOH A 268 2574 1.97 REMARK 500 REMARK 500 REMARK: NULL 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 113 77.37 65.98 REMARK 500 THR A 141 -10.31 80.13 REMARK 500 REMARK 500 REMARK: NULL DBREF 5JW8 A 29 161 UNP C9X152 C9X152_NEIM8 36 168 SEQADV 5JW8 GLY A 25 UNP C9X152 EXPRESSION TAG SEQADV 5JW8 SER A 26 UNP C9X152 EXPRESSION TAG SEQADV 5JW8 HIS A 27 UNP C9X152 EXPRESSION TAG SEQADV 5JW8 MET A 28 UNP C9X152 EXPRESSION TAG SEQRES 1 A 137 GLY SER HIS MET ALA ARG ALA GLN VAL SER GLU ALA ILE SEQRES 2 A 137 LEU LEU ALA GLU GLY GLN LYS SER ALA VAL THR GLU TYR SEQRES 3 A 137 TYR LEU ASN HIS GLY GLU TRP PRO GLY ASP ASN SER SER SEQRES 4 A 137 ALA GLY VAL ALA THR SER ALA ASP ILE LYS GLY LYS TYR SEQRES 5 A 137 VAL GLN SER VAL THR VAL ALA ASN GLY VAL ILE THR ALA SEQRES 6 A 137 GLN MET ALA SER SER ASN VAL ASN ASN GLU ILE LYS SER SEQRES 7 A 137 LYS LYS LEU SER LEU TRP ALA LYS ARG GLN ASN GLY SER SEQRES 8 A 137 VAL LYS TRP PHE CYS GLY GLN PRO VAL THR ARG THR THR SEQRES 9 A 137 ALA THR ALA THR ASP VAL ALA ALA ALA ASN GLY LYS THR SEQRES 10 A 137 ASP ASP LYS ILE ASN THR LYS HIS LEU PRO SER THR CYS SEQRES 11 A 137 ARG ASP ASP SER SER ALA SER FORMUL 2 HOH *156(H2 O) HELIX 1 AA1 ALA A 29 GLY A 42 1 14 HELIX 2 AA2 GLN A 43 GLY A 55 1 13 HELIX 3 AA3 ASP A 60 GLY A 65 1 6 HELIX 4 AA4 THR A 68 ILE A 72 5 5 HELIX 5 AA5 ASN A 97 LYS A 101 5 5 HELIX 6 AA6 ASN A 146 LEU A 150 5 5 SHEET 1 AA1 4 VAL A 77 ALA A 83 0 SHEET 2 AA1 4 VAL A 86 MET A 91 -1 O THR A 88 N THR A 81 SHEET 3 AA1 4 LYS A 104 ARG A 111 -1 O LEU A 107 N ILE A 87 SHEET 4 AA1 4 VAL A 116 GLY A 121 -1 O PHE A 119 N TRP A 108 SHEET 1 AA2 2 VAL A 124 THR A 125 0 SHEET 2 AA2 2 ALA A 135 ALA A 136 -1 O ALA A 135 N THR A 125 SSBOND 1 CYS A 120 CYS A 154 1555 1555 2.03 CRYST1 43.450 46.260 48.370 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 0.023015 0.000000 0.000000 0.00000 SCALE2 0.000000 0.021617 0.000000 0.00000 SCALE3 0.000000 0.000000 0.020674 0.00000