HEADER CELL ADHESION 24-FEB-17 5N9H TITLE STRUCTURE OF 283-LGNY-286, THE STERIC ZIPPER THAT SUPPORTS THE SELF- TITLE 2 ASSOCIATION OF P. STUARTII OMP-PST2 INTO DIMERS OF TRIMERS COMPND MOL_ID: 1; COMPND 2 MOLECULE: PORIN; COMPND 3 CHAIN: A, B, C, M; COMPND 4 FRAGMENT: DIMERIZATION DOMAIN, UNP RESIDUES 305-308; COMPND 5 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 SYNTHETIC: YES; SOURCE 3 ORGANISM_SCIENTIFIC: PROVIDENCIA STUARTII; SOURCE 4 ORGANISM_TAXID: 588 KEYWDS STERIC-ZIPPER, PORIN, MICRO-CRYSTAL, SELF-ASSOCIATION, CELL ADHESION EXPDTA X-RAY DIFFRACTION AUTHOR C.NASRALLAH,J.P.COLLETIER REVDAT 4 08-MAY-24 5N9H 1 REMARK REVDAT 3 14-MAR-18 5N9H 1 JRNL REVDAT 2 07-MAR-18 5N9H 1 JRNL REVDAT 1 21-FEB-18 5N9H 0 JRNL AUTH M.EL-KHATIB,C.NASRALLAH,J.LOPES,Q.T.TRAN,G.TETREAU, JRNL AUTH 2 H.BASBOUS,D.FENEL,B.GALLET,M.LETHIER,J.M.BOLLA,J.M.PAGES, JRNL AUTH 3 M.VIVAUDOU,M.WEIK,M.WINTERHALTER,J.P.COLLETIER JRNL TITL PORIN SELF-ASSOCIATION ENABLES CELL-TO-CELL CONTACT IN JRNL REF PROC. NATL. ACAD. SCI. V. 115 E2220 2018 JRNL REF 2 U.S.A. JRNL REFN ESSN 1091-6490 JRNL PMID 29476011 JRNL DOI 10.1073/PNAS.1714582115 REMARK 2 REMARK 2 RESOLUTION. 1.00 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 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) : 1.00 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 23.52 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 2.030 REMARK 3 COMPLETENESS FOR RANGE (%) : 89.4 REMARK 3 NUMBER OF REFLECTIONS : 4918 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.082 REMARK 3 R VALUE (WORKING SET) : 0.081 REMARK 3 FREE R VALUE : 0.096 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.000 REMARK 3 FREE R VALUE TEST SET COUNT : 246 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 23.5285 - 1.2564 0.91 2366 125 0.0716 0.0831 REMARK 3 2 1.2564 - 0.9972 0.87 2306 121 0.0971 0.1167 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 : 0.00 REMARK 3 B_SOL : 0.00 REMARK 3 REMARK 3 ERROR ESTIMATES. REMARK 3 COORDINATE ERROR (MAXIMUM-LIKELIHOOD BASED) : 0.140 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 8.970 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 1.68 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 2.60 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 0.10480 REMARK 3 B22 (A**2) : -0.42200 REMARK 3 B33 (A**2) : -0.25650 REMARK 3 B12 (A**2) : 0.37810 REMARK 3 B13 (A**2) : -0.00480 REMARK 3 B23 (A**2) : 0.36290 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 : 0.013 148 REMARK 3 ANGLE : 1.929 200 REMARK 3 CHIRALITY : 0.113 16 REMARK 3 PLANARITY : 0.007 24 REMARK 3 DIHEDRAL : 11.338 44 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 5N9H COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 24-FEB-17. REMARK 100 THE DEPOSITION ID IS D_1200003194. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 31-MAY-12 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 4 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : ESRF REMARK 200 BEAMLINE : ID23-2 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.873 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 : 4934 REMARK 200 RESOLUTION RANGE HIGH (A) : 0.997 REMARK 200 RESOLUTION RANGE LOW (A) : 47.040 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 5.500 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 89.7 REMARK 200 DATA REDUNDANCY : 2.170 REMARK 200 R MERGE (I) : 0.04000 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 14.8100 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.00 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.06 REMARK 200 COMPLETENESS FOR SHELL (%) : 87.4 REMARK 200 DATA REDUNDANCY IN SHELL : 2.12 REMARK 200 R MERGE FOR SHELL (I) : 0.15000 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 5.470 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: AB INITIO PHASING REMARK 200 SOFTWARE USED: SHELXD, SHELXE, SHELXL REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NEEDLES REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 15.40 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 1.45 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 3.2 M AMMONIUM SULFATE; 0.1 M BUFFER REMARK 280 ACID CITRIC PH4, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 293K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,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 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: TETRAMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 430 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 2700 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -15.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, B, C, M 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 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 2003 O HOH C 2001 1464 1.95 REMARK 500 O HOH B 2003 O HOH M 2001 1545 2.17 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 SO4 A 301 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue SO4 B 301 DBREF1 5N9H A 255 258 UNP A0A0L6X8Y0_PROST DBREF2 5N9H A A0A0L6X8Y0 305 308 DBREF1 5N9H B 255 258 UNP A0A0L6X8Y0_PROST DBREF2 5N9H B A0A0L6X8Y0 305 308 DBREF1 5N9H C 255 258 UNP A0A0L6X8Y0_PROST DBREF2 5N9H C A0A0L6X8Y0 305 308 DBREF1 5N9H M 255 258 UNP A0A0L6X8Y0_PROST DBREF2 5N9H M A0A0L6X8Y0 305 308 SEQRES 1 A 4 LEU GLY ASN TYR SEQRES 1 B 4 LEU GLY ASN TYR SEQRES 1 C 4 LEU GLY ASN TYR SEQRES 1 M 4 LEU GLY ASN TYR HET SO4 A 301 10 HET SO4 B 301 10 HETNAM SO4 SULFATE ION FORMUL 5 SO4 2(O4 S 2-) FORMUL 7 HOH *8(H2 O) SITE 1 AC1 6 LEU A 255 ASN A 257 HOH A2001 HOH A2002 SITE 2 AC1 6 LEU C 255 ASN C 257 SITE 1 AC2 6 LEU B 255 ASN B 257 HOH B2001 HOH B2002 SITE 2 AC2 6 LEU M 255 ASN M 257 CRYST1 4.784 11.546 47.044 90.01 90.01 90.01 P 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 0.209030 0.000036 0.000036 0.00000 SCALE2 0.000000 0.086610 0.000015 0.00000 SCALE3 0.000000 0.000000 0.021257 0.00000