10 20 30 40 50 60 70 80 1S2X - Header ----|----|----|----|----|----|----|----|----|----|----|----|----|----|----|----| Asymmetric UnitHEADER UNKNOWN FUNCTION 12-JAN-04 1S2X
TITLE CRYSTAL STRUCTURE OF CAG-Z FROM HELICOBACTER PYLORI
COMPND MOL_ID: 1; COMPND 2 MOLECULE: CAG-Z; COMPND 3 CHAIN: A; COMPND 4 ENGINEERED: YES; COMPND 5 MUTATION: YES
SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: HELICOBACTER PYLORI; SOURCE 3 ORGANISM_TAXID: 210; SOURCE 4 GENE: CAGZ; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21(DE3); SOURCE 6 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 7 EXPRESSION_SYSTEM_STRAIN: BL21 (DE3); SOURCE 8 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 9 EXPRESSION_SYSTEM_PLASMID: PGEX-4T-3
KEYWDS CAG-Z, HELICOBACTER PYLORI, CAG PATHOGENICITY ISLAND, TYPE KEYWDS 2 IV SECRETION SYSTEM, UNKNOWN FUNCTION
EXPDTA X-RAY DIFFRACTION
AUTHOR L.CENDRON,A.SEYDEL,A.ANGELINI,R.BATTISTUTTA,G.ZANOTTI
REVDAT 3 24-FEB-09 1S2X 1 VERSN REVDAT 2 10-AUG-04 1S2X 1 TITLE REVDAT 1 27-JUL-04 1S2X 0
JRNL AUTH L.CENDRON,A.SEYDEL,A.ANGELINI,R.BATTISTUTTA, JRNL AUTH 2 G.ZANOTTI JRNL TITL CRYSTAL STRUCTURE OF CAGZ, A PROTEIN FROM THE JRNL TITL 2 HELICOBACTER PYLORI PATHOGENICITY ISLAND THAT JRNL TITL 3 ENCODES FOR A TYPE IV SECRETION SYSTEM JRNL REF J.MOL.BIOL. V. 340 881 2004 JRNL REFN ISSN 0022-2836 JRNL PMID 15223328 JRNL DOI 10.1016/J.JMB.2004.05.016
REMARK 1
REMARK 2 REMARK 2 RESOLUTION. 1.90 ANGSTROMS.
REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : SHELXL-97 REMARK 3 AUTHORS : G.M.SHELDRICK REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.90 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 8.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : 2.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 88.9 REMARK 3 CROSS-VALIDATION METHOD : FREE R REMARK 3 FREE R VALUE TEST SET SELECTION : RANDOM REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT (NO CUTOFF). REMARK 3 R VALUE (WORKING + TEST SET, NO CUTOFF) : 0.245 REMARK 3 R VALUE (WORKING SET, NO CUTOFF) : 0.229 REMARK 3 FREE R VALUE (NO CUTOFF) : 0.263 REMARK 3 FREE R VALUE TEST SET SIZE (%, NO CUTOFF) : NULL REMARK 3 FREE R VALUE TEST SET COUNT (NO CUTOFF) : 1381 REMARK 3 TOTAL NUMBER OF REFLECTIONS (NO CUTOFF) : 17961 REMARK 3 REMARK 3 FIT/AGREEMENT OF MODEL FOR DATA WITH F>4SIG(F). REMARK 3 R VALUE (WORKING + TEST SET, F>4SIG(F)) : 0.229 REMARK 3 R VALUE (WORKING SET, F>4SIG(F)) : NULL REMARK 3 FREE R VALUE (F>4SIG(F)) : NULL REMARK 3 FREE R VALUE TEST SET SIZE (%, F>4SIG(F)) : NULL REMARK 3 FREE R VALUE TEST SET COUNT (F>4SIG(F)) : NULL REMARK 3 TOTAL NUMBER OF REFLECTIONS (F>4SIG(F)) : 13176 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 1463 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 0 REMARK 3 SOLVENT ATOMS : 95 REMARK 3 REMARK 3 MODEL REFINEMENT. REMARK 3 OCCUPANCY SUM OF NON-HYDROGEN ATOMS : 1556.00 REMARK 3 OCCUPANCY SUM OF HYDROGEN ATOMS : 0.00 REMARK 3 NUMBER OF DISCRETELY DISORDERED RESIDUES : 0 REMARK 3 NUMBER OF LEAST-SQUARES PARAMETERS : 6267 REMARK 3 NUMBER OF RESTRAINTS : 5971 REMARK 3 REMARK 3 RMS DEVIATIONS FROM RESTRAINT TARGET VALUES. REMARK 3 BOND LENGTHS (A) : 0.006 REMARK 3 ANGLE DISTANCES (A) : 0.020 REMARK 3 SIMILAR DISTANCES (NO TARGET VALUES) (A) : 0.000 REMARK 3 DISTANCES FROM RESTRAINT PLANES (A) : 0.022 REMARK 3 ZERO CHIRAL VOLUMES (A**3) : 0.026 REMARK 3 NON-ZERO CHIRAL VOLUMES (A**3) : 0.031 REMARK 3 ANTI-BUMPING DISTANCE RESTRAINTS (A) : 0.030 REMARK 3 RIGID-BOND ADP COMPONENTS (A**2) : 0.000 REMARK 3 SIMILAR ADP COMPONENTS (A**2) : 0.085 REMARK 3 APPROXIMATELY ISOTROPIC ADPS (A**2) : 0.000 REMARK 3 REMARK 3 BULK SOLVENT MODELING. REMARK 3 METHOD USED: NULL REMARK 3 REMARK 3 STEREOCHEMISTRY TARGET VALUES : ENGH AND HUBER REMARK 3 SPECIAL CASE: NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: ANISOTROPIC SCALING APPLIED BY THE REMARK 3 METHOD OF PARKIN, MOEZZI & HOPE, J.APPL.CRYST.28(1995)53-56
REMARK 4 REMARK 4 1S2X COMPLIES WITH FORMAT V. 3.15, 01-DEC-08
REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 16-JAN-04. REMARK 100 THE RCSB ID CODE IS RCSB021299.
REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 10-SEP-03 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 7.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : ESRF REMARK 200 BEAMLINE : ID29 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.9202 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 4 REMARK 200 INTENSITY-INTEGRATION SOFTWARE : MOSFLM REMARK 200 DATA SCALING SOFTWARE : CCP4 (SCALA) REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 18377 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.900 REMARK 200 RESOLUTION RANGE LOW (A) : 45.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 0.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 98.6 REMARK 200 DATA REDUNDANCY : 6.200 REMARK 200 R MERGE (I) : 0.05400 REMARK 200 R SYM (I) : NULL REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 5.0000 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) : 2.00 REMARK 200 COMPLETENESS FOR SHELL (%) : 92.5 REMARK 200 DATA REDUNDANCY IN SHELL : 4.10 REMARK 200 R MERGE FOR SHELL (I) : 0.24600 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 <I/SIGMA(I)> FOR SHELL : 1.700 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: MAD REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MAD REMARK 200 SOFTWARE USED: CNS REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL
REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 54.70 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.74 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: PEG 4000, ISOPROPANOL, HEPES, PH REMARK 280 7.5, VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 298K
REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 21 21 21 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X+1/2,-Y,Z+1/2 REMARK 290 3555 -X,Y+1/2,-Z+1/2 REMARK 290 4555 X+1/2,-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 15.77500 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 79.80000 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 22.32500 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 79.80000 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 15.77500 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 22.32500 REMARK 290 SMTRY3 4 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 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 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 -6 REMARK 465 SER A -5 REMARK 465 PRO A -4 REMARK 465 ASN A -3 REMARK 465 SER A -2 REMARK 465 ARG A -1 REMARK 465 THR A 180 REMARK 465 TYR A 181 REMARK 465 LEU A 182 REMARK 465 THR A 183 REMARK 465 SER A 184 REMARK 465 LEU A 185 REMARK 465 GLU A 186 REMARK 465 ARG A 187 REMARK 465 ALA A 188 REMARK 465 LYS A 189 REMARK 465 LEU A 190 REMARK 465 ILE A 191 REMARK 465 THR A 192 REMARK 465 GLN A 193 REMARK 465 LEU A 194 REMARK 465 LYS A 195 REMARK 465 LEU A 196 REMARK 465 ASN A 197 REMARK 465 LEU A 198 REMARK 465 GLU A 199
REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CLOSE CONTACTS IN SAME ASYMMETRIC UNIT REMARK 500 REMARK 500 THE FOLLOWING ATOMS ARE IN CLOSE CONTACT. REMARK 500 REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI DISTANCE REMARK 500 OD1 ASP A 41 O HOH A 1065 2.17 REMARK 500 REMARK 500 REMARK: NULL 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 ASN A 6 158.19 -49.37 REMARK 500 LYS A 177 104.31 -39.24 REMARK 500 ASN A 178 165.43 -39.68 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 IPA A 201
DBREF 1S2X A 1 199 UNP Q9JMX9 Q9JMX9_HELPY 1 199
SEQADV 1S2X GLY A -6 UNP Q9JMX9 CLONING ARTIFACT SEQADV 1S2X SER A -5 UNP Q9JMX9 CLONING ARTIFACT SEQADV 1S2X PRO A -4 UNP Q9JMX9 CLONING ARTIFACT SEQADV 1S2X ASN A -3 UNP Q9JMX9 CLONING ARTIFACT SEQADV 1S2X SER A -2 UNP Q9JMX9 CLONING ARTIFACT SEQADV 1S2X ARG A -1 UNP Q9JMX9 CLONING ARTIFACT SEQADV 1S2X VAL A 0 UNP Q9JMX9 CLONING ARTIFACT SEQADV 1S2X ASP A 1 UNP Q9JMX9 MET 1 ENGINEERED SEQADV 1S2X MSE A 21 UNP Q9JMX9 MET 21 MODIFIED RESIDUE SEQADV 1S2X MSE A 59 UNP Q9JMX9 MET 59 MODIFIED RESIDUE SEQADV 1S2X MSE A 144 UNP Q9JMX9 MET 144 MODIFIED RESIDUE SEQADV 1S2X MSE A 145 UNP Q9JMX9 MET 145 MODIFIED RESIDUE
SEQRES 1 A 206 GLY SER PRO ASN SER ARG VAL ASP GLU LEU GLY PHE ASN SEQRES 2 A 206 GLU ALA GLU ARG GLN LYS ILE LEU ASP SER ASN SER SER SEQRES 3 A 206 LEU MSE ARG ASN ALA ASN GLU VAL ARG ASP LYS PHE ILE SEQRES 4 A 206 GLN ASN TYR ALA THR SER LEU LYS ASP SER ASN ASP PRO SEQRES 5 A 206 GLN ASP PHE LEU ARG ARG VAL GLN GLU LEU ARG ILE ASN SEQRES 6 A 206 MSE GLN LYS ASN PHE ILE SER PHE ASP ALA TYR TYR ASN SEQRES 7 A 206 TYR LEU ASN ASN LEU VAL LEU ALA SER TYR ASN ARG CYS SEQRES 8 A 206 LYS GLN GLU LYS THR PHE ALA GLU SER THR ILE LYS ASN SEQRES 9 A 206 GLU LEU THR LEU GLY GLU PHE VAL ALA GLU ILE SER ASP SEQRES 10 A 206 ASN PHE ASN ASN PHE THR CYS ASP GLU VAL ALA ARG ILE SEQRES 11 A 206 SER ASP LEU VAL ALA SER TYR LEU PRO ARG GLU TYR LEU SEQRES 12 A 206 PRO PRO PHE ILE ASP GLY ASN MSE MSE GLY VAL ALA PHE SEQRES 13 A 206 GLN ILE LEU GLY ILE ASP ASP PHE GLY LYS LYS LEU ASN SEQRES 14 A 206 GLU ILE VAL GLN ASP ILE GLY THR LYS TYR ILE ILE LEU SEQRES 15 A 206 SER LYS ASN LYS THR TYR LEU THR SER LEU GLU ARG ALA SEQRES 16 A 206 LYS LEU ILE THR GLN LEU LYS LEU ASN LEU GLU
MODRES 1S2X MSE A 21 MET SELENOMETHIONINE MODRES 1S2X MSE A 59 MET SELENOMETHIONINE MODRES 1S2X MSE A 144 MET SELENOMETHIONINE MODRES 1S2X MSE A 145 MET SELENOMETHIONINE
HET MSE A 21 8 HET MSE A 59 8 HET MSE A 144 8 HET MSE A 145 8 HET IPA A 201 4
HETNAM MSE SELENOMETHIONINE HETNAM IPA ISOPROPYL ALCOHOL
HETSYN IPA 2-PROPANOL
FORMUL 1 MSE 4(C5 H11 N O2 SE) FORMUL 2 IPA C3 H8 O FORMUL 3 HOH *91(H2 O)
HELIX 1 1 ASN A 6 ASN A 17 1 12 HELIX 2 2 ASN A 23 ALA A 36 1 14 HELIX 3 3 THR A 37 SER A 42 5 6 HELIX 4 4 ASP A 44 ASN A 62 1 19 HELIX 5 5 PHE A 66 ILE A 95 1 30 HELIX 6 6 ASN A 97 SER A 129 1 33 HELIX 7 7 TYR A 130 LEU A 131 5 2 HELIX 8 8 PRO A 132 LEU A 136 5 5 HELIX 9 9 ASP A 141 LEU A 152 1 12 HELIX 10 10 GLY A 153 LYS A 177 1 25
LINK C LEU A 20 N MSE A 21 1555 1555 1.33 LINK C MSE A 21 N ARG A 22 1555 1555 1.33 LINK C ASN A 58 N MSE A 59 1555 1555 1.33 LINK C MSE A 59 N GLN A 60 1555 1555 1.33 LINK C ASN A 143 N MSE A 144 1555 1555 1.32 LINK C MSE A 144 N MSE A 145 1555 1555 1.34 LINK C MSE A 145 N GLY A 146 1555 1555 1.33
SITE 1 AC1 1 SER A 124
CRYST1 31.550 44.650 159.600 90.00 90.00 90.00 P 21 21 21 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 0.031696 0.000000 0.000000 0.00000
SCALE2 0.000000 0.022396 0.000000 0.00000
SCALE3 0.000000 0.000000 0.006266 0.00000