HEADER PEPTIDE BINDING PROTEIN 16-JUL-12 4G4W TITLE CRYSTAL STRUCTURE OF PEPTIDOGLYCAN-ASSOCIATED LIPOPROTEIN FROM TITLE 2 ACINETOBACTER BAUMANNII COMPND MOL_ID: 1; COMPND 2 MOLECULE: PEPTIDOGLYCAN-ASSOCIATED LIPOPROTEIN; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: UNP RESIDUES 75-184; COMPND 5 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: ACINETOBACTER BAUMANNII; SOURCE 3 ORGANISM_TAXID: 980514; SOURCE 4 STRAIN: TCDC-AB0715; SOURCE 5 GENE: ABTW07_3009, PAL; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 8 EXPRESSION_SYSTEM_STRAIN: BL21(DE3); SOURCE 9 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 10 EXPRESSION_SYSTEM_PLASMID: PET28A KEYWDS OMPA-LIKE DOMAIN, MEMBRANE PROTEIN, PEPTIDE BINDING PROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR W.C.LEE,J.H.SONG,J.S.PARK,H.Y.KIM REVDAT 2 15-NOV-17 4G4W 1 REMARK REVDAT 1 24-JUL-13 4G4W 0 JRNL AUTH W.C.LEE,J.S.PARK,J.H.SONG,S.I.KIM,J.C.LEE,J.CHEONG,H.Y.KIM JRNL TITL ENANTIOMER-DEPENDENT AMINO ACID BINDING AFFINITY OF JRNL TITL 2 OMPA-LIKE DOMAINS FROM ACINETOBACTER BAUMANNII JRNL TITL 3 PEPTIDOGLYCAN-ASSOCIATED LIPOPROTEIN AND OMPA JRNL REF TO BE PUBLISHED JRNL REFN REMARK 2 REMARK 2 RESOLUTION. 1.90 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : CNS 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) : 1.90 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 50.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 DATA CUTOFF HIGH (ABS(F)) : NULL REMARK 3 DATA CUTOFF LOW (ABS(F)) : NULL REMARK 3 COMPLETENESS (WORKING+TEST) (%) : 98.9 REMARK 3 NUMBER OF REFLECTIONS : 13902 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 CROSS-VALIDATION METHOD : NULL REMARK 3 FREE R VALUE TEST SET SELECTION : NULL REMARK 3 R VALUE (WORKING SET) : 0.208 REMARK 3 FREE R VALUE : 0.229 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.000 REMARK 3 FREE R VALUE TEST SET COUNT : 699 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 : 10 REMARK 3 BIN RESOLUTION RANGE HIGH (A) : 1.90 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.97 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 98.30 REMARK 3 REFLECTIONS IN BIN (WORKING SET) : 1292 REMARK 3 BIN R VALUE (WORKING SET) : 0.2774 REMARK 3 BIN FREE R VALUE : 0.2796 REMARK 3 BIN FREE R VALUE TEST SET SIZE (%) : NULL REMARK 3 BIN FREE R VALUE TEST SET COUNT : 65 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 : 859 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 22 REMARK 3 SOLVENT ATOMS : 78 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 27.76 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 4.57900 REMARK 3 B22 (A**2) : 4.57900 REMARK 3 B33 (A**2) : -9.15900 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) : NULL REMARK 3 ESD FROM SIGMAA (A) : NULL REMARK 3 LOW RESOLUTION CUTOFF (A) : NULL REMARK 3 REMARK 3 CROSS-VALIDATED ESTIMATED COORDINATE ERROR. REMARK 3 ESD FROM C-V LUZZATI PLOT (A) : NULL REMARK 3 ESD FROM C-V SIGMAA (A) : NULL REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES. REMARK 3 BOND LENGTHS (A) : 0.005 REMARK 3 BOND ANGLES (DEGREES) : NULL REMARK 3 DIHEDRAL ANGLES (DEGREES) : NULL REMARK 3 IMPROPER ANGLES (DEGREES) : NULL REMARK 3 REMARK 3 ISOTROPIC THERMAL MODEL : NULL REMARK 3 REMARK 3 ISOTROPIC THERMAL FACTOR RESTRAINTS. RMS SIGMA REMARK 3 MAIN-CHAIN BOND (A**2) : 1.319 ; 1.500 REMARK 3 MAIN-CHAIN ANGLE (A**2) : 2.027 ; 2.000 REMARK 3 SIDE-CHAIN BOND (A**2) : 2.411 ; 2.000 REMARK 3 SIDE-CHAIN ANGLE (A**2) : 3.748 ; 2.500 REMARK 3 REMARK 3 BULK SOLVENT MODELING. REMARK 3 METHOD USED : NULL REMARK 3 KSOL : NULL REMARK 3 BSOL : 41.95 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 : DNA-RNA_REP.PARAM REMARK 3 PARAMETER FILE 3 : WATER_REP.PARAM REMARK 3 PARAMETER FILE 4 : ION.PARAM REMARK 3 PARAMETER FILE 5 : CARBOHYDRATE.PARAM REMARK 3 PARAMETER FILE 6 : SO4.PARAM REMARK 3 PARAMETER FILE 7 : GOL.PARAM REMARK 3 PARAMETER FILE 8 : NULL REMARK 3 TOPOLOGY FILE 1 : PROTEIN.TOP REMARK 3 TOPOLOGY FILE 2 : DNA-RNA.TOP REMARK 3 TOPOLOGY FILE 3 : WATER.TOP REMARK 3 TOPOLOGY FILE 4 : ION.TOP REMARK 3 TOPOLOGY FILE 5 : CARBOHYDRATE.TOP REMARK 3 TOPOLOGY FILE 6 : SO4.TOP REMARK 3 TOPOLOGY FILE 7 : GOL.TOP REMARK 3 TOPOLOGY FILE 8 : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 4G4W COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 21-AUG-12. REMARK 100 THE DEPOSITION ID IS D_1000073741. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 03-JUL-11 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 4.2 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : PHOTON FACTORY REMARK 200 BEAMLINE : BL-1A REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.0 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 270 REMARK 200 INTENSITY-INTEGRATION SOFTWARE : UGUI REMARK 200 DATA SCALING SOFTWARE : SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 13980 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.900 REMARK 200 RESOLUTION RANGE LOW (A) : 50.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 98.7 REMARK 200 DATA REDUNDANCY : 6.300 REMARK 200 R MERGE (I) : 0.08300 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 15.9000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.90 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.97 REMARK 200 COMPLETENESS FOR SHELL (%) : 98.1 REMARK 200 DATA REDUNDANCY IN SHELL : 5.50 REMARK 200 R MERGE FOR SHELL (I) : 0.49700 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : NULL REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: MOLREP REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 62.27 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 3.26 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.1M PHOSPHATE CITRATE, 1.4M NAH2PO4, REMARK 280 0.4M K2HPO4, PH 4.2, VAPOR DIFFUSION, TEMPERATURE 293K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 43 21 2 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+1/2,X+1/2,Z+3/4 REMARK 290 4555 Y+1/2,-X+1/2,Z+1/4 REMARK 290 5555 -X+1/2,Y+1/2,-Z+3/4 REMARK 290 6555 X+1/2,-Y+1/2,-Z+1/4 REMARK 290 7555 Y,X,-Z REMARK 290 8555 -Y,-X,-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 57.01500 REMARK 290 SMTRY1 3 0.000000 -1.000000 0.000000 27.07000 REMARK 290 SMTRY2 3 1.000000 0.000000 0.000000 27.07000 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 85.52250 REMARK 290 SMTRY1 4 0.000000 1.000000 0.000000 27.07000 REMARK 290 SMTRY2 4 -1.000000 0.000000 0.000000 27.07000 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 28.50750 REMARK 290 SMTRY1 5 -1.000000 0.000000 0.000000 27.07000 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 27.07000 REMARK 290 SMTRY3 5 0.000000 0.000000 -1.000000 85.52250 REMARK 290 SMTRY1 6 1.000000 0.000000 0.000000 27.07000 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 27.07000 REMARK 290 SMTRY3 6 0.000000 0.000000 -1.000000 28.50750 REMARK 290 SMTRY1 7 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY2 7 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 8 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY2 8 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 8 0.000000 0.000000 -1.000000 57.01500 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 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 GLY A 71 REMARK 465 SER A 72 REMARK 465 HIS A 73 REMARK 465 MET A 74 REMARK 465 ALA A 75 REMARK 465 LEU A 76 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ALA A 201 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SO4 A 202 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SO4 A 203 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE GOL A 204 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 4G4V RELATED DB: PDB REMARK 900 RELATED ID: 4G4X RELATED DB: PDB REMARK 900 RELATED ID: 4G4Y RELATED DB: PDB REMARK 900 RELATED ID: 4G4Z RELATED DB: PDB REMARK 900 RELATED ID: 4G88 RELATED DB: PDB DBREF 4G4W A 75 184 UNP F0QP95 F0QP95_ACIBD 75 184 SEQADV 4G4W GLY A 71 UNP F0QP95 EXPRESSION TAG SEQADV 4G4W SER A 72 UNP F0QP95 EXPRESSION TAG SEQADV 4G4W HIS A 73 UNP F0QP95 EXPRESSION TAG SEQADV 4G4W MET A 74 UNP F0QP95 EXPRESSION TAG SEQRES 1 A 114 GLY SER HIS MET ALA LEU ALA LYS ARG VAL VAL HIS PHE SEQRES 2 A 114 ASP TYR ASP SER SER ASP LEU SER THR GLU ASP TYR GLN SEQRES 3 A 114 THR LEU GLN ALA HIS ALA GLN PHE LEU MET ALA ASN ALA SEQRES 4 A 114 ASN SER LYS VAL ALA LEU THR GLY HIS THR ASP GLU ARG SEQRES 5 A 114 GLY THR ARG GLU TYR ASN MET ALA LEU GLY GLU ARG ARG SEQRES 6 A 114 ALA LYS ALA VAL GLN ASN TYR LEU ILE THR SER GLY VAL SEQRES 7 A 114 ASN PRO GLN GLN LEU GLU ALA VAL SER TYR GLY LYS GLU SEQRES 8 A 114 ALA PRO VAL ASN PRO GLY HIS ASP GLU SER ALA TRP LYS SEQRES 9 A 114 GLU ASN ARG ARG VAL GLU ILE ASN TYR GLU HET ALA A 201 6 HET SO4 A 202 5 HET SO4 A 203 5 HET GOL A 204 6 HETNAM ALA ALANINE HETNAM SO4 SULFATE ION HETNAM GOL GLYCEROL HETSYN GOL GLYCERIN; PROPANE-1,2,3-TRIOL FORMUL 2 ALA C3 H7 N O2 FORMUL 3 SO4 2(O4 S 2-) FORMUL 5 GOL C3 H8 O3 FORMUL 6 HOH *78(H2 O) HELIX 1 1 SER A 91 ASN A 108 1 18 HELIX 2 2 THR A 124 SER A 146 1 23 HELIX 3 3 ASN A 149 GLN A 151 5 3 HELIX 4 4 ASP A 169 ARG A 177 1 9 SHEET 1 A 4 VAL A 80 HIS A 82 0 SHEET 2 A 4 ARG A 178 TYR A 183 -1 O VAL A 179 N VAL A 81 SHEET 3 A 4 VAL A 113 HIS A 118 -1 N ALA A 114 O ASN A 182 SHEET 4 A 4 LEU A 153 GLY A 159 1 O GLU A 154 N LEU A 115 SITE 1 AC1 10 TYR A 85 ASP A 86 THR A 119 ASP A 120 SITE 2 AC1 10 ARG A 122 TYR A 127 ASN A 128 LEU A 131 SITE 3 AC1 10 ARG A 135 ARG A 177 SITE 1 AC2 7 ARG A 122 LYS A 137 GLN A 140 GLU A 170 SITE 2 AC2 7 ARG A 177 HOH A 309 HOH A 364 SITE 1 AC3 3 HIS A 82 ASP A 94 HOH A 345 SITE 1 AC4 4 THR A 124 ARG A 125 GLU A 126 HOH A 334 CRYST1 54.140 54.140 114.030 90.00 90.00 90.00 P 43 21 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 0.018471 0.000000 0.000000 0.00000 SCALE2 0.000000 0.018471 0.000000 0.00000 SCALE3 0.000000 0.000000 0.008770 0.00000 MASTER 277 0 4 4 4 0 7 6 0 0 0 9 END