HEADER STRUCTURAL PROTEIN 12-AUG-16 5LP9 TITLE FIMA WT FROM S. FLEXNERI COMPND MOL_ID: 1; COMPND 2 MOLECULE: MAJOR TYPE 1 SUBUNIT FIMBRIN (PILIN); COMPND 3 CHAIN: A; COMPND 4 SYNONYM: TYPE-1 FIMBRIAL PROTEIN SUBUNIT A; COMPND 5 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: SHIGELLA FLEXNERI; SOURCE 3 ORGANISM_TAXID: 623; SOURCE 4 GENE: FIMA, S4465, SF4208, AJR25_020510, AJR27_013385; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21(DE3); SOURCE 6 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 7 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 8 EXPRESSION_SYSTEM_VECTOR: PET11A KEYWDS FIMA, PILUS, MONOMER, SUBUNIT, PILI, SHIGELLA, FLEXNERI, PATHOGENIC, KEYWDS 2 MAIN STRUCTURAL SUBUNIT, HIGH RESOLUTION, STRUCTURAL PROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR D.ZYLA,G.CAPITANI,A.PROTA,R.GLOCKSHUBER REVDAT 5 10-JAN-24 5LP9 1 REMARK REVDAT 4 22-APR-20 5LP9 1 REMARK REVDAT 3 25-DEC-19 5LP9 1 REMARK REVDAT 2 26-JUN-19 5LP9 1 JRNL REVDAT 1 20-DEC-17 5LP9 0 JRNL AUTH D.S.ZYLA,A.E.PROTA,G.CAPITANI,R.GLOCKSHUBER JRNL TITL ALTERNATIVE FOLDING TO A MONOMER OR HOMOPOLYMER IS A COMMON JRNL TITL 2 FEATURE OF THE TYPE 1 PILUS SUBUNIT FIMA FROM ENTEROINVASIVE JRNL TITL 3 BACTERIA. JRNL REF J.BIOL.CHEM. 2019 JRNL REFN ESSN 1083-351X JRNL PMID 31126987 JRNL DOI 10.1074/JBC.RA119.008610 REMARK 2 REMARK 2 RESOLUTION. 0.89 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.12_2829 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 : GEOSTD + MONOMER LIBRARY + CDL V1.2 REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 0.89 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 26.89 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.389 REMARK 3 COMPLETENESS FOR RANGE (%) : 91.0 REMARK 3 NUMBER OF REFLECTIONS : 89032 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.110 REMARK 3 R VALUE (WORKING SET) : 0.110 REMARK 3 FREE R VALUE : 0.126 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 1.501 REMARK 3 FREE R VALUE TEST SET COUNT : 1336 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 26.9024 - 1.9092 1.00 9741 149 0.1081 0.1286 REMARK 3 2 1.9092 - 1.5154 1.00 9629 147 0.1166 0.1256 REMARK 3 3 1.5154 - 1.3239 1.00 9641 146 0.1043 0.1151 REMARK 3 4 1.3239 - 1.2028 1.00 9559 146 0.1008 0.1228 REMARK 3 5 1.2028 - 1.1166 1.00 9641 147 0.0945 0.1021 REMARK 3 6 1.1166 - 1.0508 1.00 9531 145 0.0988 0.1140 REMARK 3 7 1.0508 - 0.9981 1.00 9634 147 0.1135 0.1351 REMARK 3 8 0.9981 - 0.9547 0.94 9019 137 0.1336 0.1598 REMARK 3 9 0.9547 - 0.9179 0.71 6770 103 0.1631 0.1592 REMARK 3 10 0.9179 - 0.8863 0.47 4531 69 0.2040 0.2196 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : FLAT BULK SOLVENT MODEL 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) : 0.050 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 13.054 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 8.26 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 19.64 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 1486 REMARK 3 ANGLE : 1.042 2075 REMARK 3 CHIRALITY : 0.085 262 REMARK 3 PLANARITY : 0.008 286 REMARK 3 DIHEDRAL : 17.237 527 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 5LP9 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 15-AUG-16. REMARK 100 THE DEPOSITION ID IS D_1200001067. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 15-JUN-15 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 2.0-3.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : SLS REMARK 200 BEAMLINE : X10SA REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.800 REMARK 200 MONOCHROMATOR : SI(111) MONOCHROMATOR 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 OCT 15, 2015 BUILT=20151231 REMARK 200 DATA SCALING SOFTWARE : XDS OCT 15, 2015 BUILT=20151231 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 89042 REMARK 200 RESOLUTION RANGE HIGH (A) : 0.850 REMARK 200 RESOLUTION RANGE LOW (A) : 26.890 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : -3.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 80.3 REMARK 200 DATA REDUNDANCY : 5.423 REMARK 200 R MERGE (I) : 0.03800 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 20.0300 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 0.85 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.00 REMARK 200 COMPLETENESS FOR SHELL (%) : 49.4 REMARK 200 DATA REDUNDANCY IN SHELL : 4.36 REMARK 200 R MERGE FOR SHELL (I) : 0.26500 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 4.460 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: PHASER 2.5.7 REMARK 200 STARTING MODEL: 2M5G MODEL 1 REMARK 200 REMARK 200 REMARK: 3-DIMENSIONAL CRYSTAL, WITH IRREGULAR SHAPE REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 29.80 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 1.75 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.1M SODIUM MALONATE, PH 3.0, 40% REMARK 280 AMMONIUM SULPHATE SATURATED AT 277 K, 23 MG/ML OF PROTEIN, 1:1 REMARK 280 MIXTURE, VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 293K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 1 21 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,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 26.89000 REMARK 290 SMTRY3 2 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: 0 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 7360 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: 0.0 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 465 LEU A 2 REMARK 470 REMARK 470 MISSING ATOM REMARK 470 THE FOLLOWING RESIDUES HAVE MISSING ATOMS (M=MODEL NUMBER; REMARK 470 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; REMARK 470 I=INSERTION CODE): REMARK 470 M RES CSSEQI ATOMS REMARK 470 LYS A 46 CG CD CE NZ REMARK 470 GLN A 47 CD OE1 NE2 REMARK 470 LYS A 158 NZ 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 HD1 HIS A 14 O HOH A 201 1.58 REMARK 500 O HOH A 213 O HOH A 368 2.01 REMARK 500 O HOH A 327 O HOH A 360 2.14 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: COVALENT BOND ANGLES 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,A3,1X,A1,I4,A1,3(1X,A4,2X),12X,F5.1) 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 ATM2 ATM3 REMARK 500 ASP A 63 CB - CG - OD2 ANGL. DEV. = -5.7 DEGREES 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 ASP A 32 78.73 -154.04 REMARK 500 LEU A 116 40.78 -90.19 REMARK 500 ALA A 119 11.14 -145.36 REMARK 500 REMARK 500 REMARK: NULL REMARK 525 REMARK 525 SOLVENT REMARK 525 REMARK 525 THE SOLVENT MOLECULES HAVE CHAIN IDENTIFIERS THAT REMARK 525 INDICATE THE POLYMER CHAIN WITH WHICH THEY ARE MOST REMARK 525 CLOSELY ASSOCIATED. THE REMARK LISTS ALL THE SOLVENT REMARK 525 MOLECULES WHICH ARE MORE THAN 5A AWAY FROM THE REMARK 525 NEAREST POLYMER CHAIN (M = MODEL NUMBER; REMARK 525 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE REMARK 525 NUMBER; I=INSERTION CODE): REMARK 525 REMARK 525 M RES CSSEQI REMARK 525 HOH A 408 DISTANCE = 7.05 ANGSTROMS DBREF 5LP9 A 2 162 UNP Q83P68 Q83P68_SHIFL 22 182 SEQADV 5LP9 MET A 1 UNP Q83P68 INITIATING METHIONINE SEQRES 1 A 162 MET LEU ALA ASP THR THR THR VAL ASN GLY GLY THR ILE SEQRES 2 A 162 HIS PHE LYS GLY GLU VAL VAL ASN ALA ALA CYS ALA VAL SEQRES 3 A 162 ASP ALA GLY SER VAL ASP GLN THR VAL GLN LEU GLY GLN SEQRES 4 A 162 VAL ARG THR ALA SER LEU LYS GLN ALA GLY ALA THR SER SEQRES 5 A 162 SER ALA VAL GLY PHE ASN ILE GLN LEU ASN ASP CYS ASP SEQRES 6 A 162 THR THR VAL ALA THR LYS ALA ALA VAL ALA PHE LEU GLY SEQRES 7 A 162 THR ALA ILE ASP ALA THR ARG THR ASP VAL LEU ALA LEU SEQRES 8 A 162 GLN SER SER ALA ALA GLY SER ALA THR ASN VAL GLY VAL SEQRES 9 A 162 GLN ILE LEU ASP ARG THR GLY ASN ALA LEU THR LEU ASP SEQRES 10 A 162 GLY ALA THR PHE SER ALA GLN THR THR LEU ASN ASN GLY SEQRES 11 A 162 THR ASN THR ILE PRO PHE GLN ALA ARG TYR TYR ALA ILE SEQRES 12 A 162 GLY GLU ALA THR PRO GLY ALA ALA ASN ALA ASP ALA THR SEQRES 13 A 162 PHE LYS VAL GLN TYR GLN FORMUL 2 HOH *208(H2 O) HELIX 1 AA1 ALA A 43 LEU A 45 5 3 SHEET 1 AA1 3 ASP A 32 GLN A 36 0 SHEET 2 AA1 3 THR A 7 LYS A 16 -1 N PHE A 15 O GLN A 33 SHEET 3 AA1 3 GLN A 39 ARG A 41 -1 O VAL A 40 N VAL A 8 SHEET 1 AA2 5 ASP A 32 GLN A 36 0 SHEET 2 AA2 5 THR A 7 LYS A 16 -1 N PHE A 15 O GLN A 33 SHEET 3 AA2 5 GLY A 149 GLN A 162 1 O ALA A 151 N GLY A 11 SHEET 4 AA2 5 LYS A 71 LEU A 77 -1 N ALA A 73 O GLN A 160 SHEET 5 AA2 5 THR A 125 THR A 126 -1 O THR A 125 N ALA A 72 SHEET 1 AA3 4 ALA A 25 VAL A 26 0 SHEET 2 AA3 4 THR A 51 CYS A 64 -1 O ASN A 62 N ALA A 25 SHEET 3 AA3 4 GLY A 130 THR A 147 -1 O ASN A 132 N LEU A 61 SHEET 4 AA3 4 THR A 100 LEU A 107 -1 N LEU A 107 O GLN A 137 SSBOND 1 CYS A 24 CYS A 64 1555 1555 2.07 CRYST1 24.140 53.780 50.290 90.00 100.34 90.00 P 1 21 1 2 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 0.041425 0.000000 0.007555 0.00000 SCALE2 0.000000 0.018594 0.000000 0.00000 SCALE3 0.000000 0.000000 0.020213 0.00000