HEADER LIPID TRANSPORT 28-DEC-15 5H9G TITLE APO-ACP FROM HELICOBACTER PYLORI COMPND MOL_ID: 1; COMPND 2 MOLECULE: ACYL CARRIER PROTEIN; COMPND 3 CHAIN: A, B; COMPND 4 SYNONYM: ACP; COMPND 5 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: HELICOBACTER PYLORI P12; SOURCE 3 ORGANISM_TAXID: 570508; SOURCE 4 STRAIN: P12; SOURCE 5 GENE: ACPP; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS ACP, FATTY ACID BIOSYNTHESIS, HELICOBACTER PYLORI, LIPID TRANSPORT EXPDTA X-RAY DIFFRACTION AUTHOR L.ZHANG,L.ZHANG,X.SHEN,H.JIANG REVDAT 3 08-NOV-23 5H9G 1 REMARK REVDAT 2 19-FEB-20 5H9G 1 REMARK REVDAT 1 28-DEC-16 5H9G 0 JRNL AUTH L.ZHANG,L.ZHANG,X.SHEN,H.JIANG JRNL TITL APO-ACP FROM HELICOBACTER PYLORI JRNL REF TO BE PUBLISHED JRNL REFN REMARK 2 REMARK 2 RESOLUTION. 2.60 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) : 2.60 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 15.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 DATA CUTOFF HIGH (ABS(F)) : NULL REMARK 3 DATA CUTOFF LOW (ABS(F)) : NULL REMARK 3 COMPLETENESS (WORKING+TEST) (%) : 99.4 REMARK 3 NUMBER OF REFLECTIONS : 6091 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 : NULL REMARK 3 R VALUE (WORKING SET) : 0.241 REMARK 3 FREE R VALUE : 0.286 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.100 REMARK 3 FREE R VALUE TEST SET COUNT : 315 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 : NULL REMARK 3 BIN RESOLUTION RANGE HIGH (A) : 2.60 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.69 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 99.20 REMARK 3 REFLECTIONS IN BIN (WORKING SET) : 564 REMARK 3 BIN R VALUE (WORKING SET) : 0.2407 REMARK 3 BIN FREE R VALUE : 0.3487 REMARK 3 BIN FREE R VALUE TEST SET SIZE (%) : 5.40 REMARK 3 BIN FREE R VALUE TEST SET COUNT : 32 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 : 1239 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 0 REMARK 3 SOLVENT ATOMS : 41 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 36.83 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -5.80200 REMARK 3 B22 (A**2) : -4.37600 REMARK 3 B33 (A**2) : 10.17800 REMARK 3 B12 (A**2) : -8.47200 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) : NULL 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) : 1.116 ; 1.500 REMARK 3 MAIN-CHAIN ANGLE (A**2) : 1.880 ; 2.000 REMARK 3 SIDE-CHAIN BOND (A**2) : 1.777 ; 2.000 REMARK 3 SIDE-CHAIN ANGLE (A**2) : 2.734 ; 2.500 REMARK 3 REMARK 3 BULK SOLVENT MODELING. REMARK 3 METHOD USED : NULL REMARK 3 KSOL : NULL REMARK 3 BSOL : 37.64 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 : CNS_TOPPAR:PROTEIN_REP.PARAM REMARK 3 PARAMETER FILE 2 : CNS_TOPPAR:WATER_REP.PARAM REMARK 3 PARAMETER FILE 3 : NULL REMARK 3 TOPOLOGY FILE 1 : NULL REMARK 3 TOPOLOGY FILE 2 : NULL REMARK 3 TOPOLOGY FILE 3 : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 5H9G COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 05-JAN-16. REMARK 100 THE DEPOSITION ID IS D_1000216702. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 15-DEC-07 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 4.5 REMARK 200 NUMBER OF CRYSTALS USED : NULL REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : PHOTON FACTORY REMARK 200 BEAMLINE : BL-17A REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : MARMOSAIC 300 MM CCD REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : HKL-2000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 6091 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.600 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 (%) : 100.0 REMARK 200 DATA REDUNDANCY : 2.400 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 8.5000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.60 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.69 REMARK 200 COMPLETENESS FOR SHELL (%) : 98.3 REMARK 200 DATA REDUNDANCY IN SHELL : 2.20 REMARK 200 R MERGE FOR SHELL (I) : 0.61300 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 1.400 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: CNS REMARK 200 STARTING MODEL: 1T8K REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 54.23 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.69 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.1 M SODIUM ACETATE TRIHYDRATE, 3.0 M REMARK 280 SODIUM CHLORIDE, PH 4.5, EVAPORATION, TEMPERATURE 277K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 31 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -Y,X-Y,Z+1/3 REMARK 290 3555 -X+Y,-X,Z+2/3 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 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 2 0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 24.31633 REMARK 290 SMTRY1 3 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 3 -0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 48.63267 REMARK 290 REMARK 290 REMARK: NULL REMARK 300 REMARK 300 BIOMOLECULE: 1, 2 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 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 350 REMARK 350 BIOMOLECULE: 2 REMARK 350 AUTHOR DETERMINED BIOLOGICAL UNIT: MONOMERIC REMARK 350 APPLY THE FOLLOWING TO CHAINS: 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 ALA A -9 REMARK 465 MET A -8 REMARK 465 GLY A -7 REMARK 465 TYR A -6 REMARK 465 LEU A -5 REMARK 465 LEU A 77 REMARK 465 ALA A 78 REMARK 465 ALA B -9 REMARK 465 MET B -8 REMARK 465 GLY B -7 REMARK 465 TYR B -6 REMARK 465 LEU B -5 REMARK 465 LYS B 76 REMARK 465 LEU B 77 REMARK 465 ALA B 78 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 VAL A 29 -71.62 -79.68 REMARK 500 ASP A 74 4.94 -53.59 REMARK 500 ALA B 26 126.77 -35.85 REMARK 500 TYR B 71 -4.92 -58.39 REMARK 500 GLU B 73 6.53 -65.68 REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 5H9H RELATED DB: PDB DBREF 5H9G A 1 78 UNP B6JLE2 ACP_HELP2 1 78 DBREF 5H9G B 1 78 UNP B6JLE2 ACP_HELP2 1 78 SEQADV 5H9G ALA A -9 UNP B6JLE2 EXPRESSION TAG SEQADV 5H9G MET A -8 UNP B6JLE2 EXPRESSION TAG SEQADV 5H9G GLY A -7 UNP B6JLE2 EXPRESSION TAG SEQADV 5H9G TYR A -6 UNP B6JLE2 EXPRESSION TAG SEQADV 5H9G LEU A -5 UNP B6JLE2 EXPRESSION TAG SEQADV 5H9G ALA A -4 UNP B6JLE2 EXPRESSION TAG SEQADV 5H9G MET A -3 UNP B6JLE2 EXPRESSION TAG SEQADV 5H9G GLY A -2 UNP B6JLE2 EXPRESSION TAG SEQADV 5H9G TYR A -1 UNP B6JLE2 EXPRESSION TAG SEQADV 5H9G LEU A 0 UNP B6JLE2 EXPRESSION TAG SEQADV 5H9G ALA B -9 UNP B6JLE2 EXPRESSION TAG SEQADV 5H9G MET B -8 UNP B6JLE2 EXPRESSION TAG SEQADV 5H9G GLY B -7 UNP B6JLE2 EXPRESSION TAG SEQADV 5H9G TYR B -6 UNP B6JLE2 EXPRESSION TAG SEQADV 5H9G LEU B -5 UNP B6JLE2 EXPRESSION TAG SEQADV 5H9G ALA B -4 UNP B6JLE2 EXPRESSION TAG SEQADV 5H9G MET B -3 UNP B6JLE2 EXPRESSION TAG SEQADV 5H9G GLY B -2 UNP B6JLE2 EXPRESSION TAG SEQADV 5H9G TYR B -1 UNP B6JLE2 EXPRESSION TAG SEQADV 5H9G LEU B 0 UNP B6JLE2 EXPRESSION TAG SEQRES 1 A 88 ALA MET GLY TYR LEU ALA MET GLY TYR LEU MET ALA LEU SEQRES 2 A 88 PHE GLU ASP ILE GLN ALA VAL ILE ALA GLU GLN LEU ASN SEQRES 3 A 88 VAL ASP ALA ALA GLN VAL THR PRO GLU ALA GLU PHE VAL SEQRES 4 A 88 LYS ASP LEU GLY ALA ASP SER LEU ASP VAL VAL GLU LEU SEQRES 5 A 88 ILE MET ALA LEU GLU GLU LYS PHE GLY ILE GLU ILE PRO SEQRES 6 A 88 ASP GLU GLN ALA GLU LYS ILE VAL ASN VAL GLY ASP VAL SEQRES 7 A 88 VAL LYS TYR ILE GLU ASP ASN LYS LEU ALA SEQRES 1 B 88 ALA MET GLY TYR LEU ALA MET GLY TYR LEU MET ALA LEU SEQRES 2 B 88 PHE GLU ASP ILE GLN ALA VAL ILE ALA GLU GLN LEU ASN SEQRES 3 B 88 VAL ASP ALA ALA GLN VAL THR PRO GLU ALA GLU PHE VAL SEQRES 4 B 88 LYS ASP LEU GLY ALA ASP SER LEU ASP VAL VAL GLU LEU SEQRES 5 B 88 ILE MET ALA LEU GLU GLU LYS PHE GLY ILE GLU ILE PRO SEQRES 6 B 88 ASP GLU GLN ALA GLU LYS ILE VAL ASN VAL GLY ASP VAL SEQRES 7 B 88 VAL LYS TYR ILE GLU ASP ASN LYS LEU ALA FORMUL 3 HOH *41(H2 O) HELIX 1 AA1 ALA A -4 ASN A 16 1 21 HELIX 2 AA2 ASP A 18 VAL A 22 5 5 HELIX 3 AA3 ASP A 35 GLY A 51 1 17 HELIX 4 AA4 PRO A 55 GLU A 60 1 6 HELIX 5 AA5 ASN A 64 ASP A 74 1 11 HELIX 6 AA6 MET B -3 ASN B 16 1 20 HELIX 7 AA7 ASP B 18 VAL B 22 5 5 HELIX 8 AA8 ASP B 35 GLY B 51 1 17 HELIX 9 AA9 PRO B 55 GLU B 60 1 6 HELIX 10 AB1 ASN B 64 GLU B 73 1 10 CRYST1 49.596 49.596 72.949 90.00 90.00 120.00 P 31 6 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 0.020163 0.011641 0.000000 0.00000 SCALE2 0.000000 0.023282 0.000000 0.00000 SCALE3 0.000000 0.000000 0.013708 0.00000