HEADER METAL BINDING PROTEIN 20-JUN-23 8T7K TITLE APO HFTA FROM TREPONEMA DENTICOLA COMPND MOL_ID: 1; COMPND 2 MOLECULE: PATHOGEN-SPECIFIC SURFACE ANTIGEN, PUTATIVE; COMPND 3 CHAIN: A; COMPND 4 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: TREPONEMA DENTICOLA ATCC 35405; SOURCE 3 ORGANISM_TAXID: 243275; SOURCE 4 GENE: TDE_1511; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21(DE3); SOURCE 6 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 7 EXPRESSION_SYSTEM_PLASMID: PET-21A KEYWDS LIPOPROTEIN, IRON TRANSPORT, PERIPLASMIC, METAL BINDING PROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR B.W.CORBETT,M.D.SUITS REVDAT 1 26-JUN-24 8T7K 0 JRNL AUTH B.W.CORBETT,M.D.SUITS JRNL TITL STRUCTURAL AND FUNCTIONAL CHARACTERIZATION OF THE JRNL TITL 2 HIGH-AFFINITY FERROUS IRON TRANSPORT PROTEIN HFTA FROM JRNL TITL 3 TREPONEMA DENTICOLA. JRNL REF TO BE PUBLISHED JRNL REFN REMARK 2 REMARK 2 RESOLUTION. 1.78 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX (1.20.1_4487: ???) 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 : ML REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.78 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 29.62 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.350 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.8 REMARK 3 NUMBER OF REFLECTIONS : 16053 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.216 REMARK 3 R VALUE (WORKING SET) : 0.215 REMARK 3 FREE R VALUE : 0.239 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.650 REMARK 3 FREE R VALUE TEST SET COUNT : 747 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 29.6200 - 3.0400 1.00 3185 154 0.1927 0.2126 REMARK 3 2 3.0400 - 2.4200 1.00 3055 149 0.2540 0.2870 REMARK 3 3 2.4200 - 2.1100 1.00 3013 152 0.2239 0.2471 REMARK 3 4 2.1100 - 1.9200 1.00 3040 157 0.2213 0.2500 REMARK 3 5 1.9200 - 1.7800 1.00 3013 135 0.2612 0.2993 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : FLAT BULK SOLVENT MODEL REMARK 3 SOLVENT RADIUS : 1.10 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) : 0.160 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 31.500 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 27.34 REMARK 3 MEAN B VALUE (OVERALL, A**2) : NULL 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 : 0.007 NULL REMARK 3 ANGLE : 0.909 NULL REMARK 3 CHIRALITY : 0.066 172 REMARK 3 PLANARITY : 0.009 227 REMARK 3 DIHEDRAL : 7.065 164 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 8T7K COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 22-JUN-23. REMARK 100 THE DEPOSITION ID IS D_1000275113. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 22-FEB-22 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : NULL REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : CHESS REMARK 200 BEAMLINE : 7B2 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.9686 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS EIGER2 X 16M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : AUTOPROC REMARK 200 DATA SCALING SOFTWARE : SCALA REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 16097 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.780 REMARK 200 RESOLUTION RANGE LOW (A) : 29.620 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 100.0 REMARK 200 DATA REDUNDANCY : 6.600 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 15.2000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.78 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.88 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 : 3.500 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: PHASER REMARK 200 STARTING MODEL: 3PJL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 48.06 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.37 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: SODIUM ACETATE, AMMONIUM SULPHATE, REMARK 280 GLYCEROL, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 291K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: C 2 2 21 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,-Y,Z+1/2 REMARK 290 3555 -X,Y,-Z+1/2 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+1/2 REMARK 290 7555 -X+1/2,Y+1/2,-Z+1/2 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 39.90150 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 39.90150 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 27.36750 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 37.48400 REMARK 290 SMTRY3 5 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 6 -1.000000 0.000000 0.000000 27.36750 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 37.48400 REMARK 290 SMTRY3 6 0.000000 0.000000 1.000000 39.90150 REMARK 290 SMTRY1 7 -1.000000 0.000000 0.000000 27.36750 REMARK 290 SMTRY2 7 0.000000 1.000000 0.000000 37.48400 REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 39.90150 REMARK 290 SMTRY1 8 1.000000 0.000000 0.000000 27.36750 REMARK 290 SMTRY2 8 0.000000 -1.000000 0.000000 37.48400 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 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 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 PHE A 74 -166.08 -163.49 REMARK 500 SER A 85 -162.13 -110.60 REMARK 500 REMARK 500 REMARK: NULL DBREF 8T7K A 53 208 UNP Q73MJ7 Q73MJ7_TREDE 53 208 SEQRES 1 A 156 PHE ASP GLU PHE PRO ILE GLY ASP GLU GLN ASP ALA GLY SEQRES 2 A 156 ILE LEU THR VAL ALA GLY VAL TYR PHE GLN PRO VAL ASP SEQRES 3 A 156 MET GLU PRO ALA GLY ASN SER LEU SER LYS ASN GLU ALA SEQRES 4 A 156 ASP CYS HIS MET GLU ALA ASP ILE SER ALA ASN GLU LYS SEQRES 5 A 156 GLY ALA THR LEU GLY TYR GLY ALA GLY ASP PHE VAL PRO SEQRES 6 A 156 TYR LEU HIS VAL LYS ALA TYR ILE GLN LYS VAL GLY SER SEQRES 7 A 156 SER LYS VAL GLN GLU VAL ALA PHE MET PRO MET ASN ALA SEQRES 8 A 156 SER ASP GLY PRO HIS TYR GLY ALA ASN VAL LYS PHE GLU SEQRES 9 A 156 GLU GLY LEU GLY LYS TYR ASN ILE LYS PHE GLU ILE LYS SEQRES 10 A 156 ALA PRO GLY ASN ASP TYR LEU LEU HIS VAL ASP LYS GLU SEQRES 11 A 156 THR GLY VAL THR GLY ARG PHE TRP THR GLU PRO ILE VAL SEQRES 12 A 156 VAL GLU TRP LYS ASP PHE GLU TRP THR GLY PRO GLN TRP FORMUL 2 HOH *53(H2 O) HELIX 1 AA1 GLU A 103 GLY A 109 5 7 HELIX 2 AA2 PRO A 171 TYR A 175 5 5 SHEET 1 AA1 3 PHE A 56 PRO A 57 0 SHEET 2 AA1 3 LEU A 67 PHE A 74 -1 O TYR A 73 N PHE A 56 SHEET 3 AA1 3 GLN A 62 ALA A 64 -1 N GLN A 62 O VAL A 69 SHEET 1 AA2 5 PHE A 56 PRO A 57 0 SHEET 2 AA2 5 LEU A 67 PHE A 74 -1 O TYR A 73 N PHE A 56 SHEET 3 AA2 5 CYS A 93 ALA A 101 -1 O SER A 100 N THR A 68 SHEET 4 AA2 5 GLY A 146 VAL A 153 -1 O TYR A 149 N ALA A 97 SHEET 5 AA2 5 MET A 139 ALA A 143 -1 N MET A 139 O GLY A 150 SHEET 1 AA3 4 GLN A 134 ALA A 137 0 SHEET 2 AA3 4 HIS A 120 LYS A 127 -1 N ALA A 123 O VAL A 136 SHEET 3 AA3 4 GLY A 160 LYS A 169 -1 O GLU A 167 N LYS A 122 SHEET 4 AA3 4 ILE A 194 TRP A 203 -1 O PHE A 201 N TYR A 162 CISPEP 1 GLU A 80 PRO A 81 0 -0.33 CRYST1 54.735 74.968 79.803 90.00 90.00 90.00 C 2 2 21 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 0.018270 0.000000 0.000000 0.00000 SCALE2 0.000000 0.013339 0.000000 0.00000 SCALE3 0.000000 0.000000 0.012531 0.00000