HEADER UNKNOWN FUNCTION 31-DEC-20 7DSG TITLE CRYSTAL STRUCTURE OF BRUCELLA ABORTUS PHIA COMPND MOL_ID: 1; COMPND 2 MOLECULE: BRUCELLA ABORTUS PHIA; COMPND 3 CHAIN: A; COMPND 4 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: BRUCELLA ABORTUS BIOVAR 1 (STRAIN 9-941); SOURCE 3 ORGANISM_TAXID: 262698; SOURCE 4 STRAIN: 9-941; SOURCE 5 GENE: BRUAB1_0102; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21(DE3); SOURCE 7 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 8 EXPRESSION_SYSTEM_STRAIN: BL21(DE3) KEYWDS T4SS, LYSOZYME INHIBITOR, PLIC, UNKNOWN FUNCTION EXPDTA X-RAY DIFFRACTION AUTHOR Y.HYUN,N.-C.HA REVDAT 2 29-NOV-23 7DSG 1 REMARK REVDAT 1 12-JAN-22 7DSG 0 JRNL AUTH Y.HYUN,N.-C.HA JRNL TITL CRYSTAL STRUCTURE OF BRUCELLA ABORTUS PHIA JRNL REF TO BE PUBLISHED JRNL REFN REMARK 2 REMARK 2 RESOLUTION. 1.90 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) : 1.90 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 45.94 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.340 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.4 REMARK 3 NUMBER OF REFLECTIONS : 17144 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.241 REMARK 3 R VALUE (WORKING SET) : 0.239 REMARK 3 FREE R VALUE : 0.261 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 10.000 REMARK 3 FREE R VALUE TEST SET COUNT : 1714 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 45.9400 - 4.3400 1.00 1301 147 0.2368 0.2424 REMARK 3 2 4.3400 - 3.4500 1.00 1300 142 0.2042 0.2090 REMARK 3 3 3.4400 - 3.0100 1.00 1301 151 0.2212 0.2333 REMARK 3 4 3.0100 - 2.7400 1.00 1297 141 0.2364 0.3194 REMARK 3 5 2.7300 - 2.5400 1.00 1270 143 0.2701 0.2769 REMARK 3 6 2.5400 - 2.3900 1.00 1315 143 0.2606 0.3637 REMARK 3 7 2.3900 - 2.2700 1.00 1286 145 0.2683 0.3394 REMARK 3 8 2.2700 - 2.1700 1.00 1313 150 0.2733 0.3108 REMARK 3 9 2.1700 - 2.0900 1.00 1280 133 0.2681 0.3649 REMARK 3 10 2.0900 - 2.0200 1.00 1290 144 0.2860 0.3231 REMARK 3 11 2.0200 - 1.9500 1.00 1277 145 0.2999 0.2692 REMARK 3 12 1.9500 - 1.9000 0.94 1200 130 0.3354 0.3789 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) : 0.267 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 30.950 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 38.63 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 45.90 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 : 0.009 699 REMARK 3 ANGLE : 0.952 949 REMARK 3 CHIRALITY : 0.058 108 REMARK 3 PLANARITY : 0.005 121 REMARK 3 DIHEDRAL : 16.397 254 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 7DSG COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 06-JAN-21. REMARK 100 THE DEPOSITION ID IS D_1300020027. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 29-MAY-20 REMARK 200 TEMPERATURE (KELVIN) : 298.15 REMARK 200 PH : NULL REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : N REMARK 200 RADIATION SOURCE : FREE ELECTRON LASER REMARK 200 BEAMLINE : NCI REMARK 200 X-RAY GENERATOR MODEL : PAL-XFEL BEAMLINE NCI REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.9795 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : RAYONIX MX225-HS REMARK 200 INTENSITY-INTEGRATION SOFTWARE : CRYSTFEL REMARK 200 DATA SCALING SOFTWARE : CRYSTFEL REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 17157 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.900 REMARK 200 RESOLUTION RANGE LOW (A) : 45.950 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 100.0 REMARK 200 DATA REDUNDANCY : 108.3 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 3.7000 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) : 1.97 REMARK 200 COMPLETENESS FOR SHELL (%) : NULL REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : NULL REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: PHENIX REMARK 200 STARTING MODEL: 4MIR REMARK 200 REMARK 200 REMARK: THE ENTRY CONTAINS FRIEDEL PAIRS IN I/F_PLUS/MINUS REMARK 200 COLUMNS. REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 46.60 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.30 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 2% TACSIMATE PH 6.5, 0.1 M BIS-TRIS PH REMARK 280 6.5, 24% (W/V) PEG 3350, VAPOR DIFFUSION, HANGING DROP, REMARK 280 TEMPERATURE 287.15K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: I 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+1/2 REMARK 290 6555 -X+1/2,-Y+1/2,Z+1/2 REMARK 290 7555 -X+1/2,Y+1/2,-Z+1/2 REMARK 290 8555 X+1/2,-Y+1/2,-Z+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 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 26.51000 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 31.05000 REMARK 290 SMTRY3 5 0.000000 0.000000 1.000000 34.14000 REMARK 290 SMTRY1 6 -1.000000 0.000000 0.000000 26.51000 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 31.05000 REMARK 290 SMTRY3 6 0.000000 0.000000 1.000000 34.14000 REMARK 290 SMTRY1 7 -1.000000 0.000000 0.000000 26.51000 REMARK 290 SMTRY2 7 0.000000 1.000000 0.000000 31.05000 REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 34.14000 REMARK 290 SMTRY1 8 1.000000 0.000000 0.000000 26.51000 REMARK 290 SMTRY2 8 0.000000 -1.000000 0.000000 31.05000 REMARK 290 SMTRY3 8 0.000000 0.000000 -1.000000 34.14000 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: TETRAMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: TETRAMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 4340 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 17300 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -33.0 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 350 BIOMT1 2 -1.000000 0.000000 0.000000 -53.02000 REMARK 350 BIOMT2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 350 BIOMT3 2 0.000000 0.000000 1.000000 0.00000 REMARK 350 BIOMT1 3 -1.000000 0.000000 0.000000 -53.02000 REMARK 350 BIOMT2 3 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT3 3 0.000000 0.000000 -1.000000 0.00000 REMARK 350 BIOMT1 4 1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT2 4 0.000000 -1.000000 0.000000 0.00000 REMARK 350 BIOMT3 4 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 ASP A 2 REMARK 465 GLU A 3 REMARK 465 GLU A 4 REMARK 465 GLN A 5 REMARK 465 PRO A 6 REMARK 465 ALA A 95 REMARK 465 ASP A 96 REMARK 465 THR A 97 REMARK 465 ALA A 98 REMARK 465 GLU A 99 REMARK 465 GLU A 100 REMARK 465 LEU A 101 REMARK 465 GLU A 102 REMARK 465 HIS A 103 REMARK 465 HIS A 104 REMARK 465 HIS A 105 REMARK 465 HIS A 106 REMARK 465 HIS A 107 REMARK 465 HIS A 108 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 ALA A 33 -55.08 -128.92 REMARK 500 REMARK 500 REMARK: NULL DBREF 7DSG A 2 100 UNP Q57FR6 Q57FR6_BRUAB 136 234 SEQADV 7DSG MET A 1 UNP Q57FR6 INITIATING METHIONINE SEQADV 7DSG LEU A 101 UNP Q57FR6 EXPRESSION TAG SEQADV 7DSG GLU A 102 UNP Q57FR6 EXPRESSION TAG SEQADV 7DSG HIS A 103 UNP Q57FR6 EXPRESSION TAG SEQADV 7DSG HIS A 104 UNP Q57FR6 EXPRESSION TAG SEQADV 7DSG HIS A 105 UNP Q57FR6 EXPRESSION TAG SEQADV 7DSG HIS A 106 UNP Q57FR6 EXPRESSION TAG SEQADV 7DSG HIS A 107 UNP Q57FR6 EXPRESSION TAG SEQADV 7DSG HIS A 108 UNP Q57FR6 EXPRESSION TAG SEQRES 1 A 108 MET ASP GLU GLU GLN PRO PRO ILE GLU ARG VAL ASP TYR SEQRES 2 A 108 ILE CYS GLU ARG SER VAL VAL VAL PRO VAL THR TYR ILE SEQRES 3 A 108 ARG SER ASN GLY ALA PRO ALA ALA ALA VAL LEU GLU VAL SEQRES 4 A 108 GLU GLY LYS MET VAL ALA LEU GLN TRP HIS GLY ASP LEU SEQRES 5 A 108 LYS LYS TYR VAL ALA ILE ASP GLU GLN ASP SER TYR ARG SEQRES 6 A 108 TRP ALA ASP ARG GLY GLY GLN ALA THR LEU SER HIS LEU SEQRES 7 A 108 GLU ALA ASP HIS THR ALA LYS GLU VAL THR LEU LEU SER SEQRES 8 A 108 ALA CYS ARG ALA ASP THR ALA GLU GLU LEU GLU HIS HIS SEQRES 9 A 108 HIS HIS HIS HIS FORMUL 2 HOH *15(H2 O) HELIX 1 AA1 GLU A 16 SER A 18 5 3 SHEET 1 AA1 9 ILE A 8 ILE A 14 0 SHEET 2 AA1 9 VAL A 20 SER A 28 -1 O TYR A 25 N GLU A 9 SHEET 3 AA1 9 ALA A 31 VAL A 39 -1 O ALA A 34 N ILE A 26 SHEET 4 AA1 9 LYS A 42 HIS A 49 -1 O LEU A 46 N ALA A 35 SHEET 5 AA1 9 LYS A 54 ALA A 57 -1 O VAL A 56 N GLN A 47 SHEET 6 AA1 9 SER A 63 ARG A 69 -1 O TRP A 66 N TYR A 55 SHEET 7 AA1 9 GLN A 72 LEU A 78 -1 O SER A 76 N ARG A 65 SHEET 8 AA1 9 VAL A 87 CYS A 93 -1 O ALA A 92 N ALA A 73 SHEET 9 AA1 9 ILE A 8 ILE A 14 -1 N ILE A 14 O CYS A 93 CRYST1 53.020 62.100 68.280 90.00 90.00 90.00 I 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 0.018861 0.000000 0.000000 0.00000 SCALE2 0.000000 0.016103 0.000000 0.00000 SCALE3 0.000000 0.000000 0.014646 0.00000