HEADER CELL ADHESION 10-OCT-24 9JW8 TITLE PILIN PILA FROM BURKHOLDERIA PSEUDOMALLEI WITH IODIDE IONS COMPND MOL_ID: 1; COMPND 2 MOLECULE: PILA; COMPND 3 CHAIN: A; COMPND 4 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: BURKHOLDERIA PSEUDOMALLEI K96243; SOURCE 3 ORGANISM_TAXID: 272560; SOURCE 4 GENE: PILA, Y036_1241; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 6 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 7 EXPRESSION_SYSTEM_PLASMID: PET-32B KEYWDS PILIN, BURKHOLDERIA PSEUDOMALLEI, ADHESION PROTEIN, CELL ADHESION EXPDTA X-RAY DIFFRACTION AUTHOR T.LOTANGCHANINTRA,K.WANGKANONT REVDAT 1 15-OCT-25 9JW8 0 JRNL AUTH T.LOTANGCHANINTRA,K.WANGKANONT JRNL TITL PILIN PILA FROM BURKHOLDERIA PSEUDOMALLEI WITH IODIDE IONS JRNL REF TO BE PUBLISHED JRNL REFN REMARK 2 REMARK 2 RESOLUTION. 1.50 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.20.1_4487 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) : 1.50 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 29.09 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.340 REMARK 3 COMPLETENESS FOR RANGE (%) : 98.9 REMARK 3 NUMBER OF REFLECTIONS : 20061 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.191 REMARK 3 R VALUE (WORKING SET) : 0.189 REMARK 3 FREE R VALUE : 0.219 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.040 REMARK 3 FREE R VALUE TEST SET COUNT : 1012 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 29.0900 - 2.8700 1.00 2822 135 0.1603 0.1969 REMARK 3 2 2.8700 - 2.2800 1.00 2698 201 0.2042 0.2468 REMARK 3 3 2.2800 - 1.9900 1.00 2769 110 0.2081 0.2178 REMARK 3 4 1.9900 - 1.8100 1.00 2749 132 0.2118 0.1858 REMARK 3 5 1.8100 - 1.6800 0.99 2718 141 0.2112 0.2421 REMARK 3 6 1.6800 - 1.5800 0.99 2675 161 0.2199 0.2561 REMARK 3 7 1.5800 - 1.5000 0.95 2618 132 0.2515 0.2919 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : FLAT BULK SOLVENT MODEL REMARK 3 SOLVENT RADIUS : 1.10 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) : 0.147 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 28.158 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 19.15 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 28.97 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 1057 REMARK 3 ANGLE : 0.964 1452 REMARK 3 CHIRALITY : 0.058 170 REMARK 3 PLANARITY : 0.009 199 REMARK 3 DIHEDRAL : 12.964 372 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : 1 REMARK 3 TLS GROUP : 1 REMARK 3 SELECTION: CHAIN A REMARK 3 ORIGIN FOR THE GROUP (A): 15.2744 2.0717 5.2746 REMARK 3 T TENSOR REMARK 3 T11: 0.0932 T22: 0.0728 REMARK 3 T33: 0.1442 T12: 0.0084 REMARK 3 T13: 0.0042 T23: 0.0091 REMARK 3 L TENSOR REMARK 3 L11: 1.7985 L22: 1.3226 REMARK 3 L33: 5.3281 L12: 0.8266 REMARK 3 L13: 1.6435 L23: 2.2886 REMARK 3 S TENSOR REMARK 3 S11: 0.2123 S12: 0.0052 S13: -0.2039 REMARK 3 S21: 0.0119 S22: 0.0550 S23: -0.1947 REMARK 3 S31: 0.1111 S32: -0.0352 S33: -0.1239 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 9JW8 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 10-OCT-24. REMARK 100 THE DEPOSITION ID IS D_1300052421. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 17-DEC-22 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 7.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : APS REMARK 200 BEAMLINE : 21-ID-F REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.97872 REMARK 200 MONOCHROMATOR : C(111) REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : RAYONIX MX-300 REMARK 200 INTENSITY-INTEGRATION SOFTWARE : MOSFLM 7.4.0 REMARK 200 DATA SCALING SOFTWARE : AIMLESS 0.7.9 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 20076 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.500 REMARK 200 RESOLUTION RANGE LOW (A) : 29.090 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.0 REMARK 200 DATA REDUNDANCY : 14.90 REMARK 200 R MERGE (I) : 0.07200 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 20.6000 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) : 1.53 REMARK 200 COMPLETENESS FOR SHELL (%) : 91.1 REMARK 200 DATA REDUNDANCY IN SHELL : 11.50 REMARK 200 R MERGE FOR SHELL (I) : 0.83800 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 3.000 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: FOURIER SYNTHESIS REMARK 200 SOFTWARE USED: PHENIX 1.20.1_4487 REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 44.06 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.20 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 100 MM HEPES, 25% PEG 4,000, PH 7.5, REMARK 280 VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 298K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 43 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,-Y,Z+1/2 REMARK 290 3555 -Y,X,Z+3/4 REMARK 290 4555 Y,-X,Z+1/4 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 25.16500 REMARK 290 SMTRY1 3 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 37.74750 REMARK 290 SMTRY1 4 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY2 4 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 12.58250 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: 100 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 7400 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 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 GLN A 107 141.46 -172.17 REMARK 500 THR A 110 71.86 50.02 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 487 DISTANCE = 7.35 ANGSTROMS REMARK 525 HOH A 488 DISTANCE = 7.75 ANGSTROMS DBREF 9JW8 A 23 167 UNP Q6J5K8 Q6J5K8_BURPE 63 207 SEQADV 9JW8 GLY A 21 UNP Q6J5K8 EXPRESSION TAG SEQADV 9JW8 SER A 22 UNP Q6J5K8 EXPRESSION TAG SEQRES 1 A 147 GLY SER ALA TYR GLN ASP TYR LEU ALA ARG SER ARG VAL SEQRES 2 A 147 GLY GLU GLY LEU ALA LEU ALA ALA SER ALA ARG LEU ALA SEQRES 3 A 147 VAL ALA GLU ASN ALA ALA SER GLY ASN GLY PHE SER GLY SEQRES 4 A 147 GLY TYR VAL SER PRO PRO ALA THR ARG ASN VAL ASP SER SEQRES 5 A 147 ILE ARG VAL ASP ASP ASP SER GLY GLN ILE VAL VAL ALA SEQRES 6 A 147 PHE THR THR ARG VAL ALA ALA ALA GLY ALA ASN THR LEU SEQRES 7 A 147 VAL LEU VAL PRO SER ALA PRO ASP GLN ALA ASP THR PRO SEQRES 8 A 147 THR ALA ARG VAL ALA LEU SER LYS GLY ALA VAL GLN ALA SEQRES 9 A 147 GLY ALA ILE THR TRP GLU CYS PHE ALA ASP GLY LYS ALA SEQRES 10 A 147 SER SER SER LEU PRO ALA PRO GLY ALA GLY PRO LEU PRO SEQRES 11 A 147 THR ASP ALA PRO THR LEU ALA GLY LYS LEU ALA PRO PRO SEQRES 12 A 147 GLU CYS ARG ALA HET IOD A 201 1 HET IOD A 202 1 HETNAM IOD IODIDE ION FORMUL 2 IOD 2(I 1-) FORMUL 4 HOH *188(H2 O) HELIX 1 AA1 SER A 22 GLY A 54 1 33 HELIX 2 AA2 ALA A 157 ALA A 161 5 5 HELIX 3 AA3 PRO A 162 ARG A 166 5 5 SHEET 1 AA1 4 VAL A 70 VAL A 75 0 SHEET 2 AA1 4 ILE A 82 PHE A 86 -1 O ALA A 85 N SER A 72 SHEET 3 AA1 4 THR A 97 PRO A 105 -1 O LEU A 98 N VAL A 84 SHEET 4 AA1 4 ARG A 114 ALA A 116 -1 O VAL A 115 N ALA A 104 SHEET 1 AA2 4 VAL A 70 VAL A 75 0 SHEET 2 AA2 4 ILE A 82 PHE A 86 -1 O ALA A 85 N SER A 72 SHEET 3 AA2 4 THR A 97 PRO A 105 -1 O LEU A 98 N VAL A 84 SHEET 4 AA2 4 THR A 128 PHE A 132 -1 O GLU A 130 N VAL A 101 SSBOND 1 CYS A 131 CYS A 165 1555 1555 2.10 CISPEP 1 ALA A 143 PRO A 144 0 1.69 CRYST1 50.420 50.420 50.330 90.00 90.00 90.00 P 43 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 0.019833 0.000000 0.000000 0.00000 SCALE2 0.000000 0.019833 0.000000 0.00000 SCALE3 0.000000 0.000000 0.019869 0.00000 CONECT 795 1019 CONECT 1019 795 MASTER 246 0 2 3 8 0 0 6 1213 1 2 12 END