PDB Short entry for 1J8R HEADER STRUCTURAL PROTEIN 22-MAY-01 1J8R TITLE BINARY COMPLEX OF THE PAPG RECEPTOR-BINDING DOMAIN BOUND TO GBO4 TITLE 2 RECEPTOR COMPND MOL_ID: 1; COMPND 2 MOLECULE: PYELONEPHRITIC ADHESIN; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: PAPG RECEPTOR-BINDING DOMAIN; COMPND 5 SYNONYM: PAPG ADHESIN; COMPND 6 OTHER_DETAILS: COMPLEXED WITH NAG-GAL-GAL-GLU SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: ESCHERICHIA COLI; SOURCE 3 ORGANISM_TAXID: 562 KEYWDS PAG ADHESIN, GBO4, STRUCTURAL GENOMICS, PSI, PROTEIN STRUCTURE KEYWDS 2 INITIATIVE, MIDWEST CENTER FOR STRUCTURAL GENOMICS, MCSG, STRUCTURAL KEYWDS 3 PROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR K.W.DODSON,J.S.PINKNER,T.ROSE,G.MAGNUSSON,S.J.HULTGREN,G.WAKSMAN, AUTHOR 2 MIDWEST CENTER FOR STRUCTURAL GENOMICS (MCSG) REVDAT 5 29-JUL-20 1J8R 1 COMPND REMARK HETNAM LINK REVDAT 5 2 1 SITE ATOM REVDAT 4 21-JUL-09 1J8R 1 HETATM REVDAT 3 24-FEB-09 1J8R 1 VERSN REVDAT 2 18-JAN-05 1J8R 1 AUTHOR KEYWDS REMARK REVDAT 1 22-JUN-01 1J8R 0 JRNL AUTH K.W.DODSON,J.S.PINKNER,T.ROSE,G.MAGNUSSON,S.J.HULTGREN, JRNL AUTH 2 G.WAKSMAN JRNL TITL STRUCTURAL BASIS OF THE INTERACTION OF THE PYELONEPHRITIC E. JRNL TITL 2 COLI ADHESIN TO ITS HUMAN KIDNEY RECEPTOR. JRNL REF CELL(CAMBRIDGE,MASS.) V. 105 733 2001 JRNL REFN ISSN 0092-8674 JRNL PMID 11440716 JRNL DOI 10.1016/S0092-8674(01)00388-9 REMARK 2 REMARK 2 RESOLUTION. 1.80 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : CNS 1.0 REMARK 3 AUTHORS : BRUNGER,ADAMS,CLORE,DELANO,GROS,GROSSE- REMARK 3 : KUNSTLEVE,JIANG,KUSZEWSKI,NILGES,PANNU, REMARK 3 : READ,RICE,SIMONSON,WARREN REMARK 3 REMARK 3 REFINEMENT TARGET : NULL REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.80 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 31.63 REMARK 3 DATA CUTOFF (SIGMA(F)) : 1.000 REMARK 3 DATA CUTOFF HIGH (ABS(F)) : 304622.070 REMARK 3 DATA CUTOFF LOW (ABS(F)) : 0.0000 REMARK 3 COMPLETENESS (WORKING+TEST) (%) : 91.0 REMARK 3 NUMBER OF REFLECTIONS : 29766 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 CROSS-VALIDATION METHOD : THROUGHOUT REMARK 3 FREE R VALUE TEST SET SELECTION : RANDOM REMARK 3 R VALUE (WORKING SET) : 0.220 REMARK 3 FREE R VALUE : 0.242 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.000 REMARK 3 FREE R VALUE TEST SET COUNT : 1489 REMARK 3 ESTIMATED ERROR OF FREE R VALUE : 0.006 REMARK 3 REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN. REMARK 3 TOTAL NUMBER OF BINS USED : 6 REMARK 3 BIN RESOLUTION RANGE HIGH (A) : 1.80 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.91 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 78.70 REMARK 3 REFLECTIONS IN BIN (WORKING SET) : 3990 REMARK 3 BIN R VALUE (WORKING SET) : 0.3980 REMARK 3 BIN FREE R VALUE : 0.4220 REMARK 3 BIN FREE R VALUE TEST SET SIZE (%) : 5.40 REMARK 3 BIN FREE R VALUE TEST SET COUNT : 226 REMARK 3 ESTIMATED ERROR OF BIN FREE R VALUE : 0.028 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 1605 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 48 REMARK 3 SOLVENT ATOMS : 182 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 14.40 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 30.10 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -1.29000 REMARK 3 B22 (A**2) : 14.53000 REMARK 3 B33 (A**2) : -13.24000 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : 0.00000 REMARK 3 B23 (A**2) : 0.00000 REMARK 3 REMARK 3 ESTIMATED COORDINATE ERROR. REMARK 3 ESD FROM LUZZATI PLOT (A) : 0.25 REMARK 3 ESD FROM SIGMAA (A) : 0.45 REMARK 3 LOW RESOLUTION CUTOFF (A) : 6.00 REMARK 3 REMARK 3 CROSS-VALIDATED ESTIMATED COORDINATE ERROR. REMARK 3 ESD FROM C-V LUZZATI PLOT (A) : 0.27 REMARK 3 ESD FROM C-V SIGMAA (A) : 0.45 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES. REMARK 3 BOND LENGTHS (A) : 0.010 REMARK 3 BOND ANGLES (DEGREES) : 1.600 REMARK 3 DIHEDRAL ANGLES (DEGREES) : 26.90 REMARK 3 IMPROPER ANGLES (DEGREES) : 0.940 REMARK 3 REMARK 3 ISOTROPIC THERMAL MODEL : RESTRAINED REMARK 3 REMARK 3 ISOTROPIC THERMAL FACTOR RESTRAINTS. RMS SIGMA REMARK 3 MAIN-CHAIN BOND (A**2) : 1.250 ; 1.500 REMARK 3 MAIN-CHAIN ANGLE (A**2) : 1.760 ; 2.000 REMARK 3 SIDE-CHAIN BOND (A**2) : 2.150 ; 2.000 REMARK 3 SIDE-CHAIN ANGLE (A**2) : 3.070 ; 2.500 REMARK 3 REMARK 3 BULK SOLVENT MODELING. REMARK 3 METHOD USED : FLAT MODEL REMARK 3 KSOL : 0.36 REMARK 3 BSOL : 52.54 REMARK 3 REMARK 3 NCS MODEL : NULL REMARK 3 REMARK 3 NCS RESTRAINTS. RMS SIGMA/WEIGHT REMARK 3 GROUP 1 POSITIONAL (A) : NULL ; NULL REMARK 3 GROUP 1 B-FACTOR (A**2) : NULL ; NULL REMARK 3 REMARK 3 PARAMETER FILE 1 : PROTEIN_REP.PARAM REMARK 3 PARAMETER FILE 2 : TETRA2.PARAM REMARK 3 PARAMETER FILE 3 : WATER_REP.PARAM REMARK 3 PARAMETER FILE 4 : NULL REMARK 3 TOPOLOGY FILE 1 : PROTEIN.TOP REMARK 3 TOPOLOGY FILE 2 : TETRA.TOPO REMARK 3 TOPOLOGY FILE 3 : WATER.TOP REMARK 3 TOPOLOGY FILE 4 : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 1J8R COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 24-MAY-01. REMARK 100 THE DEPOSITION ID IS D_1000013501. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : NULL REMARK 200 TEMPERATURE (KELVIN) : NULL REMARK 200 PH : NULL REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : APS REMARK 200 BEAMLINE : 19-BM REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : NULL REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : AREA DETECTOR REMARK 200 DETECTOR MANUFACTURER : NULL REMARK 200 INTENSITY-INTEGRATION SOFTWARE : NULL REMARK 200 DATA SCALING SOFTWARE : NULL REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 29766 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.800 REMARK 200 RESOLUTION RANGE LOW (A) : 31.630 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 0.500 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 91.0 REMARK 200 DATA REDUNDANCY : NULL REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : NULL REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.80 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.91 REMARK 200 COMPLETENESS FOR SHELL (%) : 78.7 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: MAD AT THE SE EDGE REMARK 200 SOFTWARE USED: NULL REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 67.68 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 3.81 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: NULL REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: I 2 2 2 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,-Y,Z REMARK 290 3555 -X,Y,-Z REMARK 290 4555 X,-Y,-Z REMARK 290 5555 X+1/2,Y+1/2,Z+1/2 REMARK 290 6555 -X+1/2,-Y+1/2,Z+1/2 REMARK 290 7555 -X+1/2,Y+1/2,-Z+1/2 REMARK 290 8555 X+1/2,-Y+1/2,-Z+1/2 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 0.00000 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 4 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 5 1.000000 0.000000 0.000000 27.54000 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 39.83600 REMARK 290 SMTRY3 5 0.000000 0.000000 1.000000 79.01400 REMARK 290 SMTRY1 6 -1.000000 0.000000 0.000000 27.54000 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 39.83600 REMARK 290 SMTRY3 6 0.000000 0.000000 1.000000 79.01400 REMARK 290 SMTRY1 7 -1.000000 0.000000 0.000000 27.54000 REMARK 290 SMTRY2 7 0.000000 1.000000 0.000000 39.83600 REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 79.01400 REMARK 290 SMTRY1 8 1.000000 0.000000 0.000000 27.54000 REMARK 290 SMTRY2 8 0.000000 -1.000000 0.000000 39.83600 REMARK 290 SMTRY3 8 0.000000 0.000000 -1.000000 79.01400 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 APPLY THE FOLLOWING TO CHAINS: A, B 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 CYS A 118 63.72 -158.58 REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: APC3005 RELATED DB: TARGETDB DBREF 1J8R A 1 196 UNP Q47450 Q47450_ECOLX 21 216 SEQRES 1 A 196 TRP ASN ASN ILE VAL PHE TYR SER LEU GLY ASP VAL ASN SEQRES 2 A 196 SER TYR GLN GLY GLY ASN VAL VAL ILE THR GLN ARG PRO SEQRES 3 A 196 GLN PHE ILE THR SER TRP ARG PRO GLY ILE ALA THR VAL SEQRES 4 A 196 THR TRP ASN GLN CYS ASN GLY PRO GLU PHE ALA ASP GLY SEQRES 5 A 196 PHE TRP ALA TYR TYR ARG GLU TYR ILE ALA TRP VAL VAL SEQRES 6 A 196 PHE PRO LYS LYS VAL MSE THR GLN ASN GLY TYR PRO LEU SEQRES 7 A 196 PHE ILE GLU VAL HIS ASN LYS GLY SER TRP SER GLU GLU SEQRES 8 A 196 ASN THR GLY ASP ASN ASP SER TYR PHE PHE LEU LYS GLY SEQRES 9 A 196 TYR LYS TRP ASP GLU ARG ALA PHE ASP ALA GLY ASN LEU SEQRES 10 A 196 CYS GLN LYS PRO GLY GLU ILE THR ARG LEU THR GLU LYS SEQRES 11 A 196 PHE ASP ASP ILE ILE PHE LYS VAL ALA LEU PRO ALA ASP SEQRES 12 A 196 LEU PRO LEU GLY ASP TYR SER VAL LYS ILE PRO TYR THR SEQRES 13 A 196 SER GLY MSE GLN ARG HIS PHE ALA SER TYR LEU GLY ALA SEQRES 14 A 196 ARG PHE LYS ILE PRO TYR ASN VAL ALA LYS THR LEU PRO SEQRES 15 A 196 ARG GLU ASN GLU MSE LEU PHE LEU PHE LYS ASN ILE GLY SEQRES 16 A 196 GLY MODRES 1J8R MSE A 71 MET SELENOMETHIONINE MODRES 1J8R MSE A 159 MET SELENOMETHIONINE MODRES 1J8R MSE A 187 MET SELENOMETHIONINE HET MSE A 71 8 HET MSE A 159 8 HET MSE A 187 8 HET BGC B 1 12 HET GAL B 2 11 HET GLA B 3 11 HET NGA B 4 14 HETNAM MSE SELENOMETHIONINE HETNAM BGC BETA-D-GLUCOPYRANOSE HETNAM GAL BETA-D-GALACTOPYRANOSE HETNAM GLA ALPHA-D-GALACTOPYRANOSE HETNAM NGA 2-ACETAMIDO-2-DEOXY-BETA-D-GALACTOPYRANOSE FORMUL 1 MSE 3(C5 H11 N O2 SE) FORMUL 2 BGC C6 H12 O6 FORMUL 2 GAL C6 H12 O6 FORMUL 2 GLA C6 H12 O6 FORMUL 2 NGA C8 H15 N O6 FORMUL 3 HOH *182(H2 O) HELIX 1 1 PRO A 174 LYS A 179 1 6 SHEET 1 A 7 SER A 89 GLU A 91 0 SHEET 2 A 7 SER A 98 ALA A 111 -1 O PHE A 100 N GLU A 91 SHEET 3 A 7 TYR A 56 PRO A 67 -1 O TYR A 56 N ALA A 111 SHEET 4 A 7 GLY A 147 ALA A 164 -1 N THR A 156 O VAL A 65 SHEET 5 A 7 ASN A 2 LEU A 9 -1 N ASN A 3 O PHE A 163 SHEET 6 A 7 GLY A 35 CYS A 44 -1 O THR A 38 N SER A 8 SHEET 7 A 7 ILE A 124 LEU A 127 -1 O THR A 125 N ALA A 37 SHEET 1 B 6 SER A 89 GLU A 91 0 SHEET 2 B 6 SER A 98 ALA A 111 -1 O PHE A 100 N GLU A 91 SHEET 3 B 6 TYR A 56 PRO A 67 -1 O TYR A 56 N ALA A 111 SHEET 4 B 6 GLY A 147 ALA A 164 -1 N THR A 156 O VAL A 65 SHEET 5 B 6 ASN A 185 ASN A 193 -1 N ASN A 185 O TYR A 155 SHEET 6 B 6 VAL A 12 VAL A 20 1 O ASN A 13 N LEU A 188 SHEET 1 C 4 GLN A 27 THR A 30 0 SHEET 2 C 4 ILE A 134 ALA A 139 -1 O ILE A 134 N THR A 30 SHEET 3 C 4 PRO A 77 ASN A 84 -1 O PHE A 79 N ALA A 139 SHEET 4 C 4 LYS A 69 MSE A 71 -1 O VAL A 70 N LEU A 78 SHEET 1 D 2 PHE A 49 ALA A 50 0 SHEET 2 D 2 GLY A 115 ASN A 116 -1 O GLY A 115 N ALA A 50 SSBOND 1 CYS A 44 CYS A 118 1555 1555 2.04 LINK C VAL A 70 N MSE A 71 1555 1555 1.33 LINK C MSE A 71 N THR A 72 1555 1555 1.33 LINK C GLY A 158 N MSE A 159 1555 1555 1.33 LINK C MSE A 159 N GLN A 160 1555 1555 1.32 LINK C GLU A 186 N MSE A 187 1555 1555 1.33 LINK C MSE A 187 N LEU A 188 1555 1555 1.33 LINK O4 BGC B 1 C1 GAL B 2 1555 1555 1.44 LINK O4 GAL B 2 C1 GLA B 3 1555 1555 1.43 LINK O3 GLA B 3 C1 NGA B 4 1555 1555 1.43 CRYST1 55.080 79.672 158.028 90.00 90.00 90.00 I 2 2 2 8 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 0.018155 0.000000 0.000000 0.00000 SCALE2 0.000000 0.012551 0.000000 0.00000 SCALE3 0.000000 0.000000 0.006328 0.00000