HEADER STRUCTURAL PROTEIN 07-NOV-17 6EWY TITLE RIPA PEPTIDOGLYCAN HYDROLASE (RV1477, MYCOBACTERIUM TUBERCULOSIS) N- TITLE 2 TERMINAL DOMAIN COMPND MOL_ID: 1; COMPND 2 MOLECULE: PEPTIDOGLYCAN ENDOPEPTIDASE RIPA; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: MACROPHAGE INVASION AND INTRACELLULAR PERSISTENCE PROTEIN A, COMPND 5 RESUSCITATION-PROMOTING FACTOR INTERACTION PARTNER A,RPF-INTERACTING COMPND 6 PROTEIN A; COMPND 7 EC: 3.4.-.-; COMPND 8 ENGINEERED: YES; COMPND 9 OTHER_DETAILS: RIPA-N-TERMINAL DOMAIN SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: MYCOBACTERIUM TUBERCULOSIS (STRAIN ATCC 25618 / SOURCE 3 H37RV); SOURCE 4 ORGANISM_TAXID: 83332; SOURCE 5 GENE: RIPA, RV1477; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21(DE3); SOURCE 7 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 8 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 9 EXPRESSION_SYSTEM_PLASMID: PNIC28BSA4 KEYWDS PERIPLASMIC PROTEIN, STRUCTURAL PROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR R.SCHNELL,E.M.STEINER,G.SCHNEIDER,J.GUY,G.BOURENKOV REVDAT 3 24-OCT-18 6EWY 1 JRNL REVDAT 2 16-MAY-18 6EWY 1 JRNL REVDAT 1 02-MAY-18 6EWY 0 JRNL AUTH E.M.STEINER,J.LYNGSO,J.E.GUY,G.BOURENKOV,Y.LINDQVIST, JRNL AUTH 2 T.R.SCHNEIDER,J.S.PEDERSEN,G.SCHNEIDER,R.SCHNELL JRNL TITL THE STRUCTURE OF THE N-TERMINAL MODULE OF THE CELL WALL JRNL TITL 2 HYDROLASE RIPA AND ITS ROLE IN REGULATING CATALYTIC JRNL TITL 3 ACTIVITY. JRNL REF PROTEINS V. 86 912 2018 JRNL REFN ESSN 1097-0134 JRNL PMID 29722065 JRNL DOI 10.1002/PROT.25523 REMARK 2 REMARK 2 RESOLUTION. 2.20 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.9_1692 REMARK 3 AUTHORS : PAUL ADAMS,PAVEL AFONINE,VINCENT CHEN,IAN REMARK 3 : DAVIS,KRESHNA GOPAL,RALF GROSSE-KUNSTLEVE, REMARK 3 : LI-WEI HUNG,ROBERT IMMORMINO,TOM IOERGER, REMARK 3 : AIRLIE MCCOY,ERIK MCKEE,NIGEL MORIARTY, REMARK 3 : REETAL PAI,RANDY READ,JANE RICHARDSON, REMARK 3 : DAVID RICHARDSON,TOD ROMO,JIM SACCHETTINI, REMARK 3 : NICHOLAS SAUTER,JACOB SMITH,LAURENT REMARK 3 : STORONI,TOM TERWILLIGER,PETER ZWART REMARK 3 REMARK 3 REFINEMENT TARGET : NULL REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.20 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 34.99 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.380 REMARK 3 COMPLETENESS FOR RANGE (%) : 79.5 REMARK 3 NUMBER OF REFLECTIONS : 12226 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.230 REMARK 3 R VALUE (WORKING SET) : 0.228 REMARK 3 FREE R VALUE : 0.267 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.130 REMARK 3 FREE R VALUE TEST SET COUNT : 627 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT (IN BINS). REMARK 3 BIN RESOLUTION RANGE COMPL. NWORK NFREE RWORK RFREE REMARK 3 1 2.7717 - 2.4214 0.75 2715 141 0.2555 0.3089 REMARK 3 2 2.4214 - 2.2001 0.46 1641 89 0.2500 0.3139 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : NULL REMARK 3 SOLVENT RADIUS : 1.11 REMARK 3 SHRINKAGE RADIUS : 0.90 REMARK 3 K_SOL : NULL REMARK 3 B_SOL : NULL REMARK 3 REMARK 3 ERROR ESTIMATES. REMARK 3 COORDINATE ERROR (MAXIMUM-LIKELIHOOD BASED) : 0.260 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 28.510 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 67.94 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 32.20 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : NULL REMARK 3 B22 (A**2) : NULL REMARK 3 B33 (A**2) : NULL REMARK 3 B12 (A**2) : NULL REMARK 3 B13 (A**2) : NULL REMARK 3 B23 (A**2) : NULL REMARK 3 REMARK 3 TWINNING INFORMATION. REMARK 3 FRACTION: NULL REMARK 3 OPERATOR: NULL REMARK 3 REMARK 3 DEVIATIONS FROM IDEAL VALUES. REMARK 3 RMSD COUNT REMARK 3 BOND : 0.008 1508 REMARK 3 ANGLE : 0.913 2043 REMARK 3 CHIRALITY : 0.032 243 REMARK 3 PLANARITY : 0.004 278 REMARK 3 DIHEDRAL : 15.139 556 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : NULL REMARK 3 REMARK 3 NCS DETAILS REMARK 3 NUMBER OF NCS GROUPS : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 6EWY COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 07-NOV-17. REMARK 100 THE DEPOSITION ID IS D_1200007386. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 13-JUN-15 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 5.75 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : ESRF REMARK 200 BEAMLINE : ID23-1 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.97625 REMARK 200 MONOCHROMATOR : SI (1 1 1) REMARK 200 OPTICS : MIRRORS 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 : AUTOPROC REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 12284 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.191 REMARK 200 RESOLUTION RANGE LOW (A) : 34.987 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 4.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 90.5 REMARK 200 DATA REDUNDANCY : 5.800 REMARK 200 R MERGE (I) : 0.05600 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 14.5000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.19 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.27 REMARK 200 COMPLETENESS FOR SHELL (%) : 87.3 REMARK 200 DATA REDUNDANCY IN SHELL : 5.30 REMARK 200 R MERGE FOR SHELL (I) : 0.38100 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 4.100 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: SAD REMARK 200 SOFTWARE USED: SHELXDE REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: ROD REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 0.61 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 3.15 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 42% MPD, 0.1M MES PH 5.75, VAPOR REMARK 280 DIFFUSION, SITTING DROP, TEMPERATURE 277K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: C 2 2 2 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,-Y,Z REMARK 290 3555 -X,Y,-Z REMARK 290 4555 X,-Y,-Z REMARK 290 5555 X+1/2,Y+1/2,Z REMARK 290 6555 -X+1/2,-Y+1/2,Z REMARK 290 7555 -X+1/2,Y+1/2,-Z REMARK 290 8555 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 0.00000 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 4 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 5 1.000000 0.000000 0.000000 22.45800 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 46.98000 REMARK 290 SMTRY3 5 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 6 -1.000000 0.000000 0.000000 22.45800 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 46.98000 REMARK 290 SMTRY3 6 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 7 -1.000000 0.000000 0.000000 22.45800 REMARK 290 SMTRY2 7 0.000000 1.000000 0.000000 46.98000 REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 8 1.000000 0.000000 0.000000 22.45800 REMARK 290 SMTRY2 8 0.000000 -1.000000 0.000000 46.98000 REMARK 290 SMTRY3 8 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 TOTAL BURIED SURFACE AREA: 0 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 13950 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: 0.0 KCAL/MOL 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 SER A 37 REMARK 465 MET A 38 REMARK 465 ALA A 39 REMARK 465 GLY A 241 REMARK 465 GLY A 242 REMARK 465 GLN A 243 REMARK 465 GLY A 244 REMARK 465 ALA A 245 REMARK 465 PRO A 246 REMARK 465 PRO A 247 REMARK 465 PHE A 248 REMARK 465 ARG A 249 REMARK 465 MET A 250 REMARK 465 TRP A 251 REMARK 465 ASP A 252 REMARK 465 PRO A 253 REMARK 465 GLY A 254 REMARK 465 SER A 255 REMARK 470 REMARK 470 MISSING ATOM REMARK 470 THE FOLLOWING RESIDUES HAVE MISSING ATOMS (M=MODEL NUMBER; REMARK 470 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; REMARK 470 I=INSERTION CODE): REMARK 470 M RES CSSEQI ATOMS REMARK 470 ASP A 40 CG OD1 OD2 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 OD2 ASP A 117 O HOH A 301 2.00 REMARK 500 NZ LYS A 180 O HOH A 302 2.04 REMARK 500 O HOH A 313 O HOH A 370 2.07 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 THR A 43 -4.07 -59.18 REMARK 500 VAL A 130 -87.83 -129.34 REMARK 500 REMARK 500 REMARK: NULL DBREF 6EWY A 39 255 UNP O53168 RIPA_MYCTU 39 255 SEQADV 6EWY SER A 37 UNP O53168 EXPRESSION TAG SEQADV 6EWY MET A 38 UNP O53168 EXPRESSION TAG SEQRES 1 A 219 SER MET ALA ASP PRO GLN THR ASP THR ILE ALA ALA LEU SEQRES 2 A 219 ILE ALA ASP VAL ALA LYS ALA ASN GLN ARG LEU GLN ASP SEQRES 3 A 219 LEU SER ASP GLU VAL GLN ALA GLU GLN GLU SER VAL ASN SEQRES 4 A 219 LYS ALA MET VAL ASP VAL GLU THR ALA ARG ASP ASN ALA SEQRES 5 A 219 ALA ALA ALA GLU ASP ASP LEU GLU VAL SER GLN ARG ALA SEQRES 6 A 219 VAL LYS ASP ALA ASN ALA ALA ILE ALA ALA ALA GLN HIS SEQRES 7 A 219 ARG PHE ASP THR PHE ALA ALA ALA THR TYR MET ASN GLY SEQRES 8 A 219 PRO SER VAL SER TYR LEU SER ALA SER SER PRO ASP GLU SEQRES 9 A 219 ILE ILE ALA THR VAL THR ALA ALA LYS THR LEU SER ALA SEQRES 10 A 219 SER SER GLN ALA VAL MET ALA ASN LEU GLN ARG ALA ARG SEQRES 11 A 219 THR GLU ARG VAL ASN THR GLU SER ALA ALA ARG LEU ALA SEQRES 12 A 219 LYS GLN LYS ALA ASP LYS ALA ALA ALA ASP ALA LYS ALA SEQRES 13 A 219 SER GLN ASP ALA ALA VAL ALA ALA LEU THR GLU THR ARG SEQRES 14 A 219 ARG LYS PHE ASP GLU GLN ARG GLU GLU VAL GLN ARG LEU SEQRES 15 A 219 ALA ALA GLU ARG ASP ALA ALA GLN ALA ARG LEU GLN ALA SEQRES 16 A 219 ALA ARG LEU VAL ALA TRP SER SER GLU GLY GLY GLN GLY SEQRES 17 A 219 ALA PRO PRO PHE ARG MET TRP ASP PRO GLY SER FORMUL 2 HOH *98(H2 O) HELIX 1 AA1 ASP A 44 ASN A 126 1 83 HELIX 2 AA2 SER A 137 SER A 238 1 102 CRYST1 44.916 93.960 138.672 90.00 90.00 90.00 C 2 2 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 0.022264 0.000000 0.000000 0.00000 SCALE2 0.000000 0.010643 0.000000 0.00000 SCALE3 0.000000 0.000000 0.007211 0.00000