HEADER HYDROLASE 10-DEC-20 7DNP TITLE STRUCTURE OF BRUCELLA ABORTUS SAGA COMPND MOL_ID: 1; COMPND 2 MOLECULE: SECRETION ACTIVATOR PROTEIN, HYPOTHETICAL; COMPND 3 CHAIN: A; COMPND 4 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: BRUCELLA ABORTUS BV. 1 STR. 9-941; SOURCE 3 ORGANISM_TAXID: 262698; SOURCE 4 STRAIN: 9-941; SOURCE 5 GENE: BRUAB1_0990; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21(DE3); SOURCE 7 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 8 EXPRESSION_SYSTEM_STRAIN: BL21(DE3) KEYWDS SAGA, MURAMIDASE, BRUCELLA ABORTUS, T4SS, HYDROLASE EXPDTA X-RAY DIFFRACTION AUTHOR Y.HYUN,N.-C.HA REVDAT 4 29-MAY-24 7DNP 1 REMARK REVDAT 3 13-OCT-21 7DNP 1 JRNL REVDAT 2 11-AUG-21 7DNP 1 JRNL REVDAT 1 23-JUN-21 7DNP 0 JRNL AUTH Y.HYUN,Y.BAEK,C.LEE,N.KI,J.AHN,S.RYU,N.C.HA JRNL TITL STRUCTURE AND FUNCTION OF THE AUTOLYSIN SAGA IN THE TYPE IV JRNL TITL 2 SECRETION SYSTEM OF BRUCELLA ABORTUS . JRNL REF MOL.CELLS V. 44 517 2021 JRNL REFN ISSN 1016-8478 JRNL PMID 34112742 JRNL DOI 10.14348/MOLCELLS.2021.0011 REMARK 2 REMARK 2 RESOLUTION. 2.00 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.17.1_3660 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 : GEOSTD + MONOMER LIBRARY + CDL V1.2 REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.00 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 45.63 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.650 REMARK 3 COMPLETENESS FOR RANGE (%) : 100.0 REMARK 3 NUMBER OF REFLECTIONS : 11405 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.188 REMARK 3 R VALUE (WORKING SET) : 0.186 REMARK 3 FREE R VALUE : 0.224 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.240 REMARK 3 FREE R VALUE TEST SET COUNT : 598 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 45.6300 - 3.1700 1.00 2773 162 0.1716 0.2019 REMARK 3 2 3.1700 - 2.5200 1.00 2683 153 0.2125 0.2433 REMARK 3 3 2.5200 - 2.2000 1.00 2701 127 0.1923 0.2440 REMARK 3 4 2.2000 - 2.0000 1.00 2650 156 0.1802 0.2506 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : FLAT BULK SOLVENT MODEL 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) : 0.140 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 20.887 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 23.35 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 22.44 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 : 0.003 1387 REMARK 3 ANGLE : 0.612 1875 REMARK 3 CHIRALITY : 0.039 215 REMARK 3 PLANARITY : 0.003 236 REMARK 3 DIHEDRAL : 14.964 189 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 7DNP COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 11-DEC-20. REMARK 100 THE DEPOSITION ID IS D_1300019780. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 27-MAR-20 REMARK 200 TEMPERATURE (KELVIN) : 100.15 REMARK 200 PH : NULL REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : PAL/PLS REMARK 200 BEAMLINE : 5C (4A) REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.00003 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS EIGER X 9M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : HKL-2000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 11424 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.000 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 : 30.70 REMARK 200 R MERGE (I) : 0.04900 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 67.5000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.00 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.03 REMARK 200 COMPLETENESS FOR SHELL (%) : NULL REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : 0.23900 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 15.60 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: SAD REMARK 200 SOFTWARE USED: AUTOSOL REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 40.87 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.08 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.2 M AMMONIUM ACETATE, 0.1 M SODIUM REMARK 280 ACETATE TRIHYDRATE (PH 4.1), 21% (W/V) POLYETHYLENE GLYCOL 4,000, REMARK 280 2 MM TRIS(2-CHLOROETHYL) PHOSPHATE (TCEP), VAPOR DIFFUSION, REMARK 280 HANGING DROP, TEMPERATURE 287.15K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 21 3 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 5555 Z,X,Y REMARK 290 6555 Z+1/2,-X+1/2,-Y REMARK 290 7555 -Z+1/2,-X,Y+1/2 REMARK 290 8555 -Z,X+1/2,-Y+1/2 REMARK 290 9555 Y,Z,X REMARK 290 10555 -Y,Z+1/2,-X+1/2 REMARK 290 11555 Y+1/2,-Z+1/2,-X REMARK 290 12555 -Y+1/2,-Z,X+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 39.52000 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 39.52000 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 39.52000 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 39.52000 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 39.52000 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 39.52000 REMARK 290 SMTRY3 4 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 5 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY2 5 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 5 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY1 6 0.000000 0.000000 1.000000 39.52000 REMARK 290 SMTRY2 6 -1.000000 0.000000 0.000000 39.52000 REMARK 290 SMTRY3 6 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY1 7 0.000000 0.000000 -1.000000 39.52000 REMARK 290 SMTRY2 7 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 7 0.000000 1.000000 0.000000 39.52000 REMARK 290 SMTRY1 8 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY2 8 1.000000 0.000000 0.000000 39.52000 REMARK 290 SMTRY3 8 0.000000 -1.000000 0.000000 39.52000 REMARK 290 SMTRY1 9 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY2 9 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY3 9 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY1 10 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY2 10 0.000000 0.000000 1.000000 39.52000 REMARK 290 SMTRY3 10 -1.000000 0.000000 0.000000 39.52000 REMARK 290 SMTRY1 11 0.000000 1.000000 0.000000 39.52000 REMARK 290 SMTRY2 11 0.000000 0.000000 -1.000000 39.52000 REMARK 290 SMTRY3 11 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY1 12 0.000000 -1.000000 0.000000 39.52000 REMARK 290 SMTRY2 12 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY3 12 1.000000 0.000000 0.000000 39.52000 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 MET A 1 REMARK 465 GLU A 176 REMARK 465 HIS A 177 REMARK 465 HIS A 178 REMARK 465 HIS A 179 REMARK 465 HIS A 180 REMARK 465 HIS A 181 REMARK 465 HIS A 182 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 TYR A 69 -65.28 -132.20 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 H9U A 201 DBREF 7DNP A 1 174 UNP Q57DE3 Q57DE3_BRUAB 1 174 SEQADV 7DNP LEU A 175 UNP Q57DE3 EXPRESSION TAG SEQADV 7DNP GLU A 176 UNP Q57DE3 EXPRESSION TAG SEQADV 7DNP HIS A 177 UNP Q57DE3 EXPRESSION TAG SEQADV 7DNP HIS A 178 UNP Q57DE3 EXPRESSION TAG SEQADV 7DNP HIS A 179 UNP Q57DE3 EXPRESSION TAG SEQADV 7DNP HIS A 180 UNP Q57DE3 EXPRESSION TAG SEQADV 7DNP HIS A 181 UNP Q57DE3 EXPRESSION TAG SEQADV 7DNP HIS A 182 UNP Q57DE3 EXPRESSION TAG SEQRES 1 A 182 MET ALA LYS GLY THR PHE ALA LYS ALA MET PRO HIS VAL SEQRES 2 A 182 PHE SER ASP GLU GLY GLY TYR VAL ASP HIS PRO LYS ASP SEQRES 3 A 182 PRO GLY GLY ALA THR ASN MET GLY ILE THR LEU ALA THR SEQRES 4 A 182 LEU SER ALA TRP GLU GLY ARG LYS VAL SER LYS ALA GLU SEQRES 5 A 182 VAL LYS ALA LEU THR LYS THR LYS ALA THR ASP ILE TYR SEQRES 6 A 182 ARG GLU ASN TYR TRP ASN LYS VAL ALA GLY ASP ASP LEU SEQRES 7 A 182 PRO ALA GLY VAL ASP HIS ALA THR LEU ASP PHE ALA ILE SEQRES 8 A 182 HIS SER GLY PRO ALA ARG ALA VAL LYS MET LEU GLN LYS SEQRES 9 A 182 VAL VAL GLY VAL ASP GLN ASP GLY VAL ILE GLY ALA LYS SEQRES 10 A 182 THR LEU ALA ALA VAL ARG LYS MET ALA ALA ASP ARG ILE SEQRES 11 A 182 ILE ASN GLU LEU CYS ASP ALA ARG LEU ALA TRP LEU LYS SEQRES 12 A 182 GLY LEU GLY THR PHE SER THR PHE GLY LYS GLY TRP THR SEQRES 13 A 182 SER ARG VAL SER ARG VAL ARG SER ARG ALA LEU ALA PHE SEQRES 14 A 182 SER ARG ASP SER ALA LEU GLU HIS HIS HIS HIS HIS HIS HET H9U A 201 48 HETNAM H9U (2R)-2-[[(2S)-2-[[(2R)-2-[(2R,3S,4R,5R,6S)-5-ACETAMIDO- HETNAM 2 H9U 3-[(2S,3R,4R,5S,6R)-3-ACETAMIDO-6-(HYDROXYMETHYL)-4,5- HETNAM 3 H9U BIS(OXIDANYL)OXAN-2-YL]OXY-2-(HYDROXYMETHYL)-6- HETNAM 4 H9U OXIDANYL-OXAN-4- HETNAM 5 H9U YL]OXYPROPANOYL]AMINO]PROPANOYL]AMINO]PENTANEDIOIC HETNAM 6 H9U ACID FORMUL 2 H9U C27 H44 N4 O17 FORMUL 3 HOH *70(H2 O) HELIX 1 AA1 GLY A 4 GLY A 18 1 15 HELIX 2 AA2 LEU A 37 GLY A 45 1 9 HELIX 3 AA3 SER A 49 ALA A 55 1 7 HELIX 4 AA4 THR A 57 TYR A 69 1 13 HELIX 5 AA5 TRP A 70 ALA A 74 5 5 HELIX 6 AA6 GLY A 81 GLY A 94 1 14 HELIX 7 AA7 GLY A 94 GLY A 107 1 14 HELIX 8 AA8 GLY A 115 LYS A 124 1 10 HELIX 9 AA9 ALA A 126 LYS A 143 1 18 HELIX 10 AB1 GLY A 144 GLY A 146 5 3 HELIX 11 AB2 THR A 147 ARG A 171 1 25 SHEET 1 AA1 3 TYR A 20 VAL A 21 0 SHEET 2 AA1 3 THR A 31 ASN A 32 -1 O THR A 31 N VAL A 21 SHEET 3 AA1 3 ILE A 35 THR A 36 -1 O ILE A 35 N ASN A 32 SITE 1 AC1 18 LYS A 3 GLY A 34 THR A 36 THR A 39 SITE 2 AC1 18 TYR A 65 TYR A 69 ILE A 91 HIS A 92 SITE 3 AC1 18 SER A 93 GLY A 94 TRP A 141 LEU A 142 SITE 4 AC1 18 LEU A 145 PHE A 151 TRP A 155 HOH A 308 SITE 5 AC1 18 HOH A 317 HOH A 354 CRYST1 79.040 79.040 79.040 90.00 90.00 90.00 P 21 3 12 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 0.012652 0.000000 0.000000 0.00000 SCALE2 0.000000 0.012652 0.000000 0.00000 SCALE3 0.000000 0.000000 0.012652 0.00000