HEADER SUGAR BINDING PROTEIN 31-MAR-15 4Z3H TITLE CRYSTAL STRUCTURE OF THE LECTIN DOMAIN OF PAPG FROM E. COLI BI47 IN TITLE 2 COMPLEX WITH 4-METHOXYPHENYL BETA-D-GALABIOSE IN SPACE GROUP P21 COMPND MOL_ID: 1; COMPND 2 MOLECULE: PAPG, LECTIN DOMAIN; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: RESIDUES 20-216; COMPND 5 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: ESCHERICHIA COLI; SOURCE 3 ORGANISM_TAXID: 562; SOURCE 4 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21(DE3); SOURCE 5 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 6 EXPRESSION_SYSTEM_VARIANT: ADA494; SOURCE 7 EXPRESSION_SYSTEM_PLASMID: PET-22B KEYWDS UPEC, URINARY TRACT INFECTION, FIMBRIAL ADHESIN, ADHESIN, TYPE I KEYWDS 2 PILI, PAPG, CARBOHYDRATE BINDING, SUGAR BINDING PROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR R.P.JAKOB,G.NAVARRA,P.ZIHLMANN,K.STANGIER,R.C.PRESTON,S.RABBANI, AUTHOR 2 T.MAIER,B.ERNST REVDAT 3 10-JAN-24 4Z3H 1 HETSYN LINK REVDAT 2 29-JUL-20 4Z3H 1 COMPND REMARK HETNAM LINK REVDAT 2 2 1 SITE ATOM REVDAT 1 13-APR-16 4Z3H 0 JRNL AUTH G.NAVARRA,P.ZIHLMANN,R.P.JAKOB,K.STANGIER,R.C.PRESTON, JRNL AUTH 2 S.RABBANI,T.MAIER,B.ERNST JRNL TITL AN UNEXPECTED WAY NATURE IMPROVES SOLVATION ENTROPY JRNL REF TO BE PUBLISHED JRNL REFN REMARK 2 REMARK 2 RESOLUTION. 1.50 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : BUSTER 2.10.0 REMARK 3 AUTHORS : BRICOGNE,BLANC,BRANDL,FLENSBURG,KELLER, REMARK 3 : PACIOREK,ROVERSI,SHARFF,SMART,VONRHEIN, REMARK 3 : WOMACK,MATTHEWS,TEN EYCK,TRONRUD REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.50 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 19.89 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 96.5 REMARK 3 NUMBER OF REFLECTIONS : 33318 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 CROSS-VALIDATION METHOD : FREE R-VALUE REMARK 3 FREE R VALUE TEST SET SELECTION : RANDOM REMARK 3 R VALUE (WORKING + TEST SET) : 0.151 REMARK 3 R VALUE (WORKING SET) : 0.150 REMARK 3 FREE R VALUE : 0.178 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.060 REMARK 3 FREE R VALUE TEST SET COUNT : 1686 REMARK 3 ESTIMATED ERROR OF FREE R VALUE : NULL REMARK 3 REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN. REMARK 3 TOTAL NUMBER OF BINS USED : 17 REMARK 3 BIN RESOLUTION RANGE HIGH (ANGSTROMS) : 1.50 REMARK 3 BIN RESOLUTION RANGE LOW (ANGSTROMS) : 1.55 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 96.50 REMARK 3 REFLECTIONS IN BIN (WORKING + TEST SET) : 2567 REMARK 3 BIN R VALUE (WORKING + TEST SET) : 0.2061 REMARK 3 REFLECTIONS IN BIN (WORKING SET) : 2448 REMARK 3 BIN R VALUE (WORKING SET) : 0.2033 REMARK 3 BIN FREE R VALUE : 0.2651 REMARK 3 BIN FREE R VALUE TEST SET SIZE (%) : 4.64 REMARK 3 BIN FREE R VALUE TEST SET COUNT : 119 REMARK 3 ESTIMATED ERROR OF BIN FREE R VALUE : NULL REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 1608 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 31 REMARK 3 SOLVENT ATOMS : 307 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 17.41 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 20.93 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -3.65950 REMARK 3 B22 (A**2) : 1.03940 REMARK 3 B33 (A**2) : 2.62000 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : 2.03640 REMARK 3 B23 (A**2) : 0.00000 REMARK 3 REMARK 3 ESTIMATED COORDINATE ERROR. REMARK 3 ESD FROM LUZZATI PLOT (A) : 0.158 REMARK 3 DPI (BLOW EQ-10) BASED ON R VALUE (A) : 0.067 REMARK 3 DPI (BLOW EQ-9) BASED ON FREE R VALUE (A) : 0.068 REMARK 3 DPI (CRUICKSHANK) BASED ON R VALUE (A) : 0.063 REMARK 3 DPI (CRUICKSHANK) BASED ON FREE R VALUE (A) : 0.066 REMARK 3 REMARK 3 REFERENCES: BLOW, D. (2002) ACTA CRYST D58, 792-797 REMARK 3 CRUICKSHANK, D.W.J. (1999) ACTA CRYST D55, 583-601 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.967 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.960 REMARK 3 REMARK 3 NUMBER OF GEOMETRIC FUNCTION TERMS DEFINED : 15 REMARK 3 TERM COUNT WEIGHT FUNCTION. REMARK 3 BOND LENGTHS : 1726 ; 2.000 ; HARMONIC REMARK 3 BOND ANGLES : 2358 ; 2.000 ; HARMONIC REMARK 3 TORSION ANGLES : 567 ; 2.000 ; SINUSOIDAL REMARK 3 TRIGONAL CARBON PLANES : 40 ; 2.000 ; HARMONIC REMARK 3 GENERAL PLANES : 249 ; 5.000 ; HARMONIC REMARK 3 ISOTROPIC THERMAL FACTORS : 1726 ; 20.000 ; HARMONIC REMARK 3 BAD NON-BONDED CONTACTS : NULL ; NULL ; NULL REMARK 3 IMPROPER TORSIONS : NULL ; NULL ; NULL REMARK 3 PSEUDOROTATION ANGLES : NULL ; NULL ; NULL REMARK 3 CHIRAL IMPROPER TORSION : 221 ; 5.000 ; SEMIHARMONIC REMARK 3 SUM OF OCCUPANCIES : NULL ; NULL ; NULL REMARK 3 UTILITY DISTANCES : NULL ; NULL ; NULL REMARK 3 UTILITY ANGLES : NULL ; NULL ; NULL REMARK 3 UTILITY TORSION : NULL ; NULL ; NULL REMARK 3 IDEAL-DIST CONTACT TERM : 2077 ; 4.000 ; SEMIHARMONIC REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES. REMARK 3 BOND LENGTHS (A) : 0.010 REMARK 3 BOND ANGLES (DEGREES) : 1.03 REMARK 3 PEPTIDE OMEGA TORSION ANGLES (DEGREES) : 4.39 REMARK 3 OTHER TORSION ANGLES (DEGREES) : 14.74 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : 1 REMARK 3 REMARK 3 TLS GROUP : 1 REMARK 3 SELECTION: { A|* } REMARK 3 ORIGIN FOR THE GROUP (A): 5.0815 -9.3668 -10.8520 REMARK 3 T TENSOR REMARK 3 T11: -0.0118 T22: -0.0295 REMARK 3 T33: -0.0230 T12: 0.0040 REMARK 3 T13: 0.0039 T23: 0.0030 REMARK 3 L TENSOR REMARK 3 L11: 0.3249 L22: 0.4598 REMARK 3 L33: 0.7947 L12: 0.1481 REMARK 3 L13: 0.0467 L23: -0.4556 REMARK 3 S TENSOR REMARK 3 S11: -0.0033 S12: 0.0123 S13: -0.0107 REMARK 3 S21: 0.0069 S22: 0.0030 S23: -0.0095 REMARK 3 S31: -0.0197 S32: 0.0012 S33: 0.0003 REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 4Z3H COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 01-APR-15. REMARK 100 THE DEPOSITION ID IS D_1000208530. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 02-SEP-13 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : NULL REMARK 200 NUMBER OF CRYSTALS USED : NULL REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : SLS REMARK 200 BEAMLINE : X06SA REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.00000 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS PILATUS 6M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : XSCALE REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 33318 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.500 REMARK 200 RESOLUTION RANGE LOW (A) : 19.890 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 96.5 REMARK 200 DATA REDUNDANCY : 6.700 REMARK 200 R MERGE (I) : 0.07500 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 15.2000 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) : 1.55 REMARK 200 COMPLETENESS FOR SHELL (%) : 87.4 REMARK 200 DATA REDUNDANCY IN SHELL : 6.40 REMARK 200 R MERGE FOR SHELL (I) : 0.61000 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 2.900 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: 1J8S REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 48.66 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.40 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 10 % PEG 10000, VAPOR DIFFUSION, REMARK 280 SITTING DROP, TEMPERATURE 297K 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 26.88500 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 SOFTWARE DETERMINED QUATERNARY STRUCTURE: MONOMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 730 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 9720 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: 8.0 KCAL/MOL 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 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 196 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 69.89 -154.43 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 607 DISTANCE = 6.22 ANGSTROMS DBREF 4Z3H A 0 196 UNP T7DCJ2 T7DCJ2_ECOLX 20 216 SEQADV 4Z3H MET A -1 UNP T7DCJ2 EXPRESSION TAG SEQADV 4Z3H GLN A 109 UNP T7DCJ2 GLU 129 CONFLICT SEQRES 1 A 198 MET ALA TRP ASN ASN ILE VAL PHE TYR SER LEU GLY ASP SEQRES 2 A 198 VAL ASN SER TYR GLN GLY GLY ASN VAL VAL ILE THR GLN SEQRES 3 A 198 ARG PRO GLN PHE ILE THR SER TRP ARG PRO GLY ILE ALA SEQRES 4 A 198 THR VAL THR TRP ASN GLN CYS ASN GLY PRO GLU PHE ALA SEQRES 5 A 198 ASP GLY SER TRP ALA TYR TYR ARG GLU TYR ILE ALA TRP SEQRES 6 A 198 VAL VAL PHE PRO LYS LYS VAL MET THR LYS ASN GLY TYR SEQRES 7 A 198 PRO LEU PHE ILE GLU VAL HIS ASN LYS GLY SER TRP SER SEQRES 8 A 198 GLU GLU ASN THR GLY ASP ASN ASP SER TYR PHE PHE LEU SEQRES 9 A 198 LYS GLY TYR LYS TRP ASP GLN ARG ALA PHE ASP THR ALA SEQRES 10 A 198 ASN LEU CYS GLN LYS PRO GLY GLU THR THR ARG LEU THR SEQRES 11 A 198 GLU LYS PHE ASP ASP ILE ILE PHE LYS VAL ALA LEU PRO SEQRES 12 A 198 ALA ASP LEU PRO LEU GLY ASP TYR SER VAL THR ILE PRO SEQRES 13 A 198 TYR THR SER GLY ILE GLN ARG HIS PHE ALA SER TYR LEU SEQRES 14 A 198 GLY ALA ARG PHE LYS ILE PRO TYR ASN VAL ALA LYS THR SEQRES 15 A 198 LEU PRO ARG GLU ASN GLU MET LEU PHE LEU PHE LYS ASN SEQRES 16 A 198 ILE GLY GLY HET GAL B 1 11 HET GLA B 2 11 HET 4KS A 201 9 HETNAM GAL BETA-D-GALACTOPYRANOSE HETNAM GLA ALPHA-D-GALACTOPYRANOSE HETNAM 4KS 4-METHOXYPHENOL HETSYN GAL BETA-D-GALACTOSE; D-GALACTOSE; GALACTOSE HETSYN GLA ALPHA-D-GALACTOSE; D-GALACTOSE; GALACTOSE; ALPHA D- HETSYN 2 GLA GALACTOSE FORMUL 2 GAL C6 H12 O6 FORMUL 2 GLA C6 H12 O6 FORMUL 3 4KS C7 H8 O2 FORMUL 4 HOH *307(H2 O) HELIX 1 AA1 PRO A 174 LYS A 179 1 6 SHEET 1 AA1 6 VAL A 12 VAL A 20 0 SHEET 2 AA1 6 ASN A 185 ASN A 193 1 O LEU A 190 N GLY A 17 SHEET 3 AA1 6 GLY A 147 ALA A 164 -1 N VAL A 151 O PHE A 189 SHEET 4 AA1 6 TYR A 56 PRO A 67 -1 N ILE A 61 O GLN A 160 SHEET 5 AA1 6 SER A 98 ALA A 111 -1 O TYR A 99 N PHE A 66 SHEET 6 AA1 6 SER A 89 GLU A 91 -1 N SER A 89 O LEU A 102 SHEET 1 AA2 6 VAL A 12 VAL A 20 0 SHEET 2 AA2 6 ASN A 185 ASN A 193 1 O LEU A 190 N GLY A 17 SHEET 3 AA2 6 GLY A 147 ALA A 164 -1 N VAL A 151 O PHE A 189 SHEET 4 AA2 6 ASN A 2 LEU A 9 -1 N VAL A 5 O ARG A 161 SHEET 5 AA2 6 GLY A 35 CYS A 44 -1 O THR A 38 N SER A 8 SHEET 6 AA2 6 THR A 124 LEU A 127 -1 O THR A 125 N ALA A 37 SHEET 1 AA3 4 GLN A 27 THR A 30 0 SHEET 2 AA3 4 ILE A 134 ALA A 139 -1 O ILE A 134 N THR A 30 SHEET 3 AA3 4 PRO A 77 ASN A 84 -1 N GLU A 81 O LYS A 137 SHEET 4 AA3 4 LYS A 69 MET A 71 -1 N VAL A 70 O LEU A 78 SHEET 1 AA4 2 PHE A 49 ALA A 50 0 SHEET 2 AA4 2 ALA A 115 ASN A 116 -1 O ALA A 115 N ALA A 50 SSBOND 1 CYS A 44 CYS A 118 1555 1555 2.03 LINK O1 4KS A 201 C1 GAL B 1 1555 1555 1.40 LINK O4 GAL B 1 C1 GLA B 2 1555 1555 1.45 CRYST1 47.350 53.770 48.320 90.00 117.58 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 0.021119 0.000000 0.011032 0.00000 SCALE2 0.000000 0.018598 0.000000 0.00000 SCALE3 0.000000 0.000000 0.023349 0.00000