HEADER HYDROLASE 08-JUN-10 3NE0 TITLE STRUCTURE AND FUNCTIONAL REGULATION OF RIPA, A MYCOBACTERIAL ENZYME TITLE 2 ESSENTIAL FOR DAUGHTER CELL SEPARATION COMPND MOL_ID: 1; COMPND 2 MOLECULE: RESUSCITATION PROMOTING FACTOR INTERACTING PROTEIN A; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: UNP RESIDUES 263-472; COMPND 5 SYNONYM: INVASION PROTEIN; COMPND 6 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: MYCOBACTERIUM TUBERCULOSIS; SOURCE 3 ORGANISM_TAXID: 83332; SOURCE 4 STRAIN: H37RV; SOURCE 5 GENE: RV1477; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 8 EXPRESSION_SYSTEM_VECTOR_TYPE: PETM-30; SOURCE 9 EXPRESSION_SYSTEM_VECTOR: PLASMID KEYWDS CELL WALL, PEPTIDOGLYCAN, TUBERCULOSIS, HYDROLASE EXPDTA X-RAY DIFFRACTION AUTHOR A.RUGGIERO,F.SQUEGLIA,R.BERISIO REVDAT 2 21-FEB-24 3NE0 1 SEQADV REVDAT 1 22-SEP-10 3NE0 0 JRNL AUTH A.RUGGIERO,D.MARASCO,F.SQUEGLIA,S.SOLDINI,E.PEDONE,C.PEDONE, JRNL AUTH 2 R.BERISIO JRNL TITL STRUCTURE AND FUNCTIONAL REGULATION OF RIPA, A MYCOBACTERIAL JRNL TITL 2 ENZYME ESSENTIAL FOR DAUGHTER CELL SEPARATION. JRNL REF STRUCTURE V. 18 1184 2010 JRNL REFN ISSN 0969-2126 JRNL PMID 20826344 JRNL DOI 10.1016/J.STR.2010.06.007 REMARK 2 REMARK 2 RESOLUTION. 1.00 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) : 1.00 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 10.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 91.7 REMARK 3 CROSS-VALIDATION METHOD : NULL 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) : 0.111 REMARK 3 R VALUE (WORKING SET, NO CUTOFF) : 0.106 REMARK 3 FREE R VALUE (NO CUTOFF) : 0.137 REMARK 3 FREE R VALUE TEST SET SIZE (%, NO CUTOFF) : NULL REMARK 3 FREE R VALUE TEST SET COUNT (NO CUTOFF) : 4295 REMARK 3 TOTAL NUMBER OF REFLECTIONS (NO CUTOFF) : 81445 REMARK 3 REMARK 3 FIT/AGREEMENT OF MODEL FOR DATA WITH F>4SIG(F). REMARK 3 R VALUE (WORKING + TEST SET, F>4SIG(F)) : 0.106 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)) : 74275 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 1543 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 0 REMARK 3 SOLVENT ATOMS : 390 REMARK 3 REMARK 3 MODEL REFINEMENT. REMARK 3 OCCUPANCY SUM OF NON-HYDROGEN ATOMS : 1934.0 REMARK 3 OCCUPANCY SUM OF HYDROGEN ATOMS : 1526.0 REMARK 3 NUMBER OF DISCRETELY DISORDERED RESIDUES : 2 REMARK 3 NUMBER OF LEAST-SQUARES PARAMETERS : 17484 REMARK 3 NUMBER OF RESTRAINTS : 7222 REMARK 3 REMARK 3 RMS DEVIATIONS FROM RESTRAINT TARGET VALUES. REMARK 3 BOND LENGTHS (A) : 0.019 REMARK 3 ANGLE DISTANCES (A) : 0.031 REMARK 3 SIMILAR DISTANCES (NO TARGET VALUES) (A) : 0.000 REMARK 3 DISTANCES FROM RESTRAINT PLANES (A) : 0.030 REMARK 3 ZERO CHIRAL VOLUMES (A**3) : 0.096 REMARK 3 NON-ZERO CHIRAL VOLUMES (A**3) : 0.105 REMARK 3 ANTI-BUMPING DISTANCE RESTRAINTS (A) : 0.117 REMARK 3 RIGID-BOND ADP COMPONENTS (A**2) : 0.000 REMARK 3 SIMILAR ADP COMPONENTS (A**2) : 0.000 REMARK 3 APPROXIMATELY ISOTROPIC ADPS (A**2) : 0.103 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: NULL REMARK 4 REMARK 4 3NE0 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 09-JUN-10. REMARK 100 THE DEPOSITION ID IS D_1000059710. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 30-JUN-08 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 5.6 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : ESRF REMARK 200 BEAMLINE : BM14 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.9737, 0.9785, 0.9787, 0.9737 REMARK 200 MONOCHROMATOR : SI(111) MONOCHROMATOR. REMARK 200 OPTICS : MIRRORS REMARK 200 REMARK 200 DETECTOR TYPE : IMAGE PLATE REMARK 200 DETECTOR MANUFACTURER : MAR SCANNER 345 MM PLATE REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : HKL-2000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 85882 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.000 REMARK 200 RESOLUTION RANGE LOW (A) : 30.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 0.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 96.5 REMARK 200 DATA REDUNDANCY : NULL REMARK 200 R MERGE (I) : 0.08000 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 19.7000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.00 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.04 REMARK 200 COMPLETENESS FOR SHELL (%) : 72.6 REMARK 200 DATA REDUNDANCY IN SHELL : 3.10 REMARK 200 R MERGE FOR SHELL (I) : 0.29200 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 3.000 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: MAD REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MAD REMARK 200 SOFTWARE USED: SHELX REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 32.42 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 1.82 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 8% (V/V) 2-PROPANOL, 16% (W/V) REMARK 280 PEG4000, 60 MM SODIUM CITRATE TRIHYDRATE BUFFER, PH 5.6, REMARK 280 EVAPORATION, TEMPERATURE 293K 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 18.43300 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 33.96550 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 32.78000 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 33.96550 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 18.43300 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 32.78000 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 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 997 REMARK 465 ALA A 998 REMARK 465 MET A 999 REMARK 465 GLY A 1000 REMARK 465 TRP A 1001 REMARK 465 ASP A 1002 REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: COVALENT BOND LENGTHS REMARK 500 REMARK 500 THE STEREOCHEMICAL PARAMETERS OF THE FOLLOWING RESIDUES REMARK 500 HAVE VALUES WHICH DEVIATE FROM EXPECTED VALUES BY MORE REMARK 500 THAN 6*RMSD (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 500 IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 STANDARD TABLE: REMARK 500 FORMAT: (10X,I3,1X,2(A3,1X,A1,I4,A1,1X,A4,3X),1X,F6.3) REMARK 500 REMARK 500 EXPECTED VALUES PROTEIN: ENGH AND HUBER, 1999 REMARK 500 EXPECTED VALUES NUCLEIC ACID: CLOWNEY ET AL 1996 REMARK 500 REMARK 500 M RES CSSEQI ATM1 RES CSSEQI ATM2 DEVIATION REMARK 500 GLY A1003 N GLY A1003 CA -0.094 REMARK 500 GLY A1003 CA GLY A1003 C 0.111 REMARK 500 GLN A1054 CD GLN A1054 NE2 -0.174 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: COVALENT BOND ANGLES REMARK 500 REMARK 500 THE STEREOCHEMICAL PARAMETERS OF THE FOLLOWING RESIDUES REMARK 500 HAVE VALUES WHICH DEVIATE FROM EXPECTED VALUES BY MORE REMARK 500 THAN 6*RMSD (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 500 IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 STANDARD TABLE: REMARK 500 FORMAT: (10X,I3,1X,A3,1X,A1,I4,A1,3(1X,A4,2X),12X,F5.1) REMARK 500 REMARK 500 EXPECTED VALUES PROTEIN: ENGH AND HUBER, 1999 REMARK 500 EXPECTED VALUES NUCLEIC ACID: CLOWNEY ET AL 1996 REMARK 500 REMARK 500 M RES CSSEQI ATM1 ATM2 ATM3 REMARK 500 GLY A1003 N - CA - C ANGL. DEV. = 16.7 DEGREES REMARK 500 MET A1011 CG - SD - CE ANGL. DEV. = 10.9 DEGREES REMARK 500 ARG A1044 NE - CZ - NH1 ANGL. DEV. = -3.6 DEGREES REMARK 500 ARG A1044 NE - CZ - NH2 ANGL. DEV. = 5.1 DEGREES REMARK 500 ARG A1071 NE - CZ - NH2 ANGL. DEV. = -3.0 DEGREES REMARK 500 ARG A1078 NE - CZ - NH1 ANGL. DEV. = -4.3 DEGREES REMARK 500 ARG A1086 CD - NE - CZ ANGL. DEV. = 12.4 DEGREES REMARK 500 ARG A1087 NE - CZ - NH1 ANGL. DEV. = 3.1 DEGREES REMARK 500 ARG A1191 NE - CZ - NH2 ANGL. DEV. = -3.1 DEGREES REMARK 500 MET A1200 CA - CB - CG ANGL. DEV. = 10.3 DEGREES 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 MET A1011 57.46 -91.62 REMARK 500 ASP A1111 -118.31 57.47 REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 3EO5 RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF THE RESUSCITATION PROMOTING FACTOR RPFB DBREF 3NE0 A 1001 1210 UNP O53168 O53168_MYCTU 263 472 SEQADV 3NE0 A UNP O53168 GLY 997 EXPRESSION TAG SEQADV 3NE0 A UNP O53168 ALA 998 EXPRESSION TAG SEQADV 3NE0 A UNP O53168 MET 999 EXPRESSION TAG SEQADV 3NE0 A UNP O53168 GLY 1000 EXPRESSION TAG SEQRES 1 A 214 GLY ALA MET GLY TRP ASP GLY LEU TRP ASP PRO THR LEU SEQRES 2 A 214 PRO MET ILE PRO SER ALA ASN ILE PRO GLY ASP PRO ILE SEQRES 3 A 214 ALA VAL VAL ASN GLN VAL LEU GLY ILE SER ALA THR SER SEQRES 4 A 214 ALA GLN VAL THR ALA ASN MET GLY ARG LYS PHE LEU GLU SEQRES 5 A 214 GLN LEU GLY ILE LEU GLN PRO THR ASP THR GLY ILE THR SEQRES 6 A 214 ASN ALA PRO ALA GLY SER ALA GLN GLY ARG ILE PRO ARG SEQRES 7 A 214 VAL TYR GLY ARG GLN ALA SER GLU TYR VAL ILE ARG ARG SEQRES 8 A 214 GLY MET SER GLN ILE GLY VAL PRO TYR SER TRP GLY GLY SEQRES 9 A 214 GLY ASN ALA ALA GLY PRO SER LYS GLY ILE ASP SER GLY SEQRES 10 A 214 ALA GLY THR VAL GLY PHE ASP CYS SER GLY LEU VAL LEU SEQRES 11 A 214 TYR SER PHE ALA GLY VAL GLY ILE LYS LEU PRO HIS TYR SEQRES 12 A 214 SER GLY SER GLN TYR ASN LEU GLY ARG LYS ILE PRO SER SEQRES 13 A 214 SER GLN MET ARG ARG GLY ASP VAL ILE PHE TYR GLY PRO SEQRES 14 A 214 ASN GLY SER GLN HIS VAL THR ILE TYR LEU GLY ASN GLY SEQRES 15 A 214 GLN MET LEU GLU ALA PRO ASP VAL GLY LEU LYS VAL ARG SEQRES 16 A 214 VAL ALA PRO VAL ARG THR ALA GLY MET THR PRO TYR VAL SEQRES 17 A 214 VAL ARG TYR ILE GLU TYR FORMUL 2 HOH *390(H2 O) HELIX 1 1 SER A 1035 LEU A 1050 1 16 HELIX 2 2 PRO A 1073 VAL A 1075 5 3 HELIX 3 3 TYR A 1076 SER A 1090 1 15 HELIX 4 4 ILE A 1110 ALA A 1114 5 5 HELIX 5 5 ASP A 1120 GLY A 1131 1 12 HELIX 6 6 TYR A 1139 ASN A 1145 1 7 HELIX 7 7 SER A 1153 MET A 1155 5 3 HELIX 8 8 GLY A 1164 SER A 1168 5 5 SHEET 1 A 2 ILE A1022 ASN A1026 0 SHEET 2 A 2 ILE A1031 THR A1034 -1 O ILE A1031 N ASN A1026 SHEET 1 B 2 SER A1107 LYS A1108 0 SHEET 2 B 2 VAL A1117 GLY A1118 -1 O GLY A1118 N SER A1107 SHEET 1 C 2 ARG A1148 PRO A1151 0 SHEET 2 C 2 TYR A1203 ARG A1206 -1 O VAL A1204 N ILE A1150 SHEET 1 D 4 VAL A1160 TYR A1163 0 SHEET 2 D 4 HIS A1170 GLY A1176 -1 O THR A1172 N ILE A1161 SHEET 3 D 4 GLN A1179 GLU A1182 -1 O GLN A1179 N LEU A1175 SHEET 4 D 4 ARG A1191 PRO A1194 -1 O ALA A1193 N MET A1180 CRYST1 36.866 65.560 67.931 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 0.027125 0.000000 0.000000 0.00000 SCALE2 0.000000 0.015253 0.000000 0.00000 SCALE3 0.000000 0.000000 0.014721 0.00000