HEADER METAL TRANSPORT 03-AUG-19 6Q1C TITLE APO YFEA EXTRACTED FROM THE E. COLI PERIPLASM COMPND MOL_ID: 1; COMPND 2 MOLECULE: PERIPLASMIC CHELATED IRON-BINDING PROTEIN YFEA; COMPND 3 CHAIN: A; COMPND 4 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: YERSINIA PESTIS; SOURCE 3 ORGANISM_TAXID: 632; SOURCE 4 GENE: YFEA, YPO2439, Y1897, YP_2227; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 6 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS YERSINIA PESTIS, SUBSTRATE BINDING PROTEIN, SBP, YFEA, METAL KEYWDS 2 TRANSPORT EXPDTA X-RAY DIFFRACTION AUTHOR C.D.RADKA,S.L.LABIUK,L.J.DELUCAS,S.G.ALLER REVDAT 4 11-OCT-23 6Q1C 1 REMARK REVDAT 3 25-SEP-19 6Q1C 1 JRNL REVDAT 2 18-SEP-19 6Q1C 1 JRNL REVDAT 1 04-SEP-19 6Q1C 0 JRNL AUTH C.D.RADKA,S.L.LABIUK,L.J.DELUCAS,S.G.ALLER JRNL TITL STRUCTURES OF THE SUBSTRATE-BINDING PROTEIN YFEA IN APO AND JRNL TITL 2 ZINC-RECONSTITUTED HOLO FORMS. JRNL REF ACTA CRYSTALLOGR D STRUCT V. 75 831 2019 JRNL REF 2 BIOL JRNL REFN ISSN 2059-7983 JRNL PMID 31478906 JRNL DOI 10.1107/S2059798319010866 REMARK 2 REMARK 2 RESOLUTION. 1.76 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.14_3260 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) : 1.76 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 38.47 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.380 REMARK 3 COMPLETENESS FOR RANGE (%) : 94.6 REMARK 3 NUMBER OF REFLECTIONS : 43168 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.194 REMARK 3 R VALUE (WORKING SET) : 0.190 REMARK 3 FREE R VALUE : 0.239 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 8.320 REMARK 3 FREE R VALUE TEST SET COUNT : 3592 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 38.4000 - 5.2103 0.96 1542 139 0.1699 0.2525 REMARK 3 2 5.2103 - 4.1372 0.95 1524 140 0.1466 0.1898 REMARK 3 3 4.1372 - 3.6146 0.98 1566 145 0.1638 0.2328 REMARK 3 4 3.6146 - 3.2843 0.98 1583 150 0.1841 0.2211 REMARK 3 5 3.2843 - 3.0490 0.96 1553 141 0.1990 0.2521 REMARK 3 6 3.0490 - 2.8693 0.94 1530 134 0.2071 0.2127 REMARK 3 7 2.8693 - 2.7257 0.95 1528 144 0.2061 0.2318 REMARK 3 8 2.7257 - 2.6071 0.96 1554 142 0.1902 0.2405 REMARK 3 9 2.6071 - 2.5067 0.97 1534 136 0.1998 0.1987 REMARK 3 10 2.5067 - 2.4202 0.97 1584 147 0.1919 0.2272 REMARK 3 11 2.4202 - 2.3446 0.98 1544 145 0.2096 0.1998 REMARK 3 12 2.3446 - 2.2776 0.96 1525 137 0.1892 0.2442 REMARK 3 13 2.2776 - 2.2176 0.93 1522 138 0.2064 0.2846 REMARK 3 14 2.2176 - 2.1635 0.92 1502 141 0.2159 0.2588 REMARK 3 15 2.1635 - 2.1143 0.92 1437 129 0.2232 0.2972 REMARK 3 16 2.1143 - 2.0693 0.94 1547 137 0.2197 0.2922 REMARK 3 17 2.0693 - 2.0279 0.96 1562 138 0.2245 0.2454 REMARK 3 18 2.0279 - 1.9897 0.96 1514 137 0.2257 0.2545 REMARK 3 19 1.9897 - 1.9541 0.97 1570 147 0.2393 0.3176 REMARK 3 20 1.9541 - 1.9210 0.98 1558 142 0.2485 0.3518 REMARK 3 21 1.9210 - 1.8900 0.97 1597 144 0.2634 0.3420 REMARK 3 22 1.8900 - 1.8610 0.97 1585 140 0.2415 0.2761 REMARK 3 23 1.8610 - 1.8336 0.95 1490 137 0.2616 0.2841 REMARK 3 24 1.8336 - 1.8078 0.93 1493 127 0.2568 0.3263 REMARK 3 25 1.8078 - 1.7833 0.86 1407 124 0.2620 0.3035 REMARK 3 26 1.7833 - 1.7602 0.76 1225 111 0.2855 0.3291 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) : 0.240 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 25.150 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 35.80 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 : NULL NULL REMARK 3 ANGLE : NULL NULL REMARK 3 CHIRALITY : NULL NULL REMARK 3 PLANARITY : NULL NULL REMARK 3 DIHEDRAL : NULL NULL 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 6Q1C COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 06-AUG-19. REMARK 100 THE DEPOSITION ID IS D_1000243432. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 07-APR-17 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 6.3 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : APS REMARK 200 BEAMLINE : 23-ID-D REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.28242 REMARK 200 MONOCHROMATOR : DOUBLE CRYSTAL CRYO-COOLED REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS PILATUS3 6M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 V712 REMARK 200 DATA SCALING SOFTWARE : SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 43178 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.760 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 (%) : 98.5 REMARK 200 DATA REDUNDANCY : 3.500 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 35.4000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.76 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.79 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: PHASER REMARK 200 STARTING MODEL: PDB ENTRY 5UXS REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 28.72 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 1.73 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 20 MM BIS-TRIS, PH 6.3, 50 MM SODIUM REMARK 280 CHLORIDE, 0.05% W/V SODIUM AZIDE, 30% W/V PEG4000, VAPOR REMARK 280 DIFFUSION, TEMPERATURE 293.15K 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 20.00850 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 56.63150 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 26.21300 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 56.63150 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 20.00850 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 26.21300 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 TOTAL BURIED SURFACE AREA: 0 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 12440 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 MET A 1 REMARK 465 ILE A 2 REMARK 465 GLU A 3 REMARK 465 ARG A 4 REMARK 465 LEU A 5 REMARK 465 ASN A 6 REMARK 465 SER A 7 REMARK 465 PRO A 8 REMARK 465 PHE A 9 REMARK 465 LEU A 10 REMARK 465 ARG A 11 REMARK 465 ALA A 12 REMARK 465 ALA A 13 REMARK 465 ALA A 14 REMARK 465 LEU A 15 REMARK 465 PHE A 16 REMARK 465 THR A 17 REMARK 465 ILE A 18 REMARK 465 VAL A 19 REMARK 465 ALA A 20 REMARK 465 PHE A 21 REMARK 465 SER A 22 REMARK 465 SER A 23 REMARK 465 LEU A 24 REMARK 465 ILE A 25 REMARK 465 SER A 26 REMARK 465 THR A 27 REMARK 465 ALA A 28 REMARK 465 ALA A 29 REMARK 465 LEU A 30 REMARK 465 ALA A 31 REMARK 465 GLU A 32 REMARK 465 ASN A 33 REMARK 465 ASN A 34 REMARK 465 PRO A 35 REMARK 465 SER A 36 REMARK 465 ASP A 37 REMARK 465 THR A 38 REMARK 465 ALA A 39 REMARK 465 PRO A 226 REMARK 465 ILE A 227 REMARK 465 ASN A 228 REMARK 465 ALA A 229 REMARK 465 GLU A 230 REMARK 465 GLN A 231 REMARK 465 GLN A 232 REMARK 465 GLY A 233 REMARK 465 ILE A 234 REMARK 465 PRO A 235 REMARK 465 GLN A 236 REMARK 465 GLN A 237 REMARK 465 VAL A 238 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 A 99 28.50 49.22 REMARK 500 HIS A 141 49.52 -80.31 REMARK 500 REMARK 500 REMARK: NULL DBREF 6Q1C A 1 311 UNP Q56952 YFEA_YERPE 1 311 SEQRES 1 A 311 MET ILE GLU ARG LEU ASN SER PRO PHE LEU ARG ALA ALA SEQRES 2 A 311 ALA LEU PHE THR ILE VAL ALA PHE SER SER LEU ILE SER SEQRES 3 A 311 THR ALA ALA LEU ALA GLU ASN ASN PRO SER ASP THR ALA SEQRES 4 A 311 LYS LYS PHE LYS VAL VAL THR THR PHE THR ILE ILE GLN SEQRES 5 A 311 ASP ILE ALA GLN ASN ILE ALA GLY ASP VAL ALA VAL VAL SEQRES 6 A 311 GLU SER ILE THR LYS PRO GLY ALA GLU ILE HIS ASP TYR SEQRES 7 A 311 GLN PRO THR PRO ARG ASP ILE VAL LYS ALA GLN SER ALA SEQRES 8 A 311 ASP LEU ILE LEU TRP ASN GLY MET ASN LEU GLU ARG TRP SEQRES 9 A 311 PHE GLU LYS PHE PHE GLU SER ILE LYS ASP VAL PRO SER SEQRES 10 A 311 ALA VAL VAL THR ALA GLY ILE THR PRO LEU PRO ILE ARG SEQRES 11 A 311 GLU GLY PRO TYR SER GLY ILE ALA ASN PRO HIS ALA TRP SEQRES 12 A 311 MET SER PRO SER ASN ALA LEU ILE TYR ILE GLU ASN ILE SEQRES 13 A 311 ARG LYS ALA LEU VAL GLU HIS ASP PRO ALA HIS ALA GLU SEQRES 14 A 311 THR TYR ASN ARG ASN ALA GLN ALA TYR ALA GLU LYS ILE SEQRES 15 A 311 LYS ALA LEU ASP ALA PRO LEU ARG GLU ARG LEU SER ARG SEQRES 16 A 311 ILE PRO ALA GLU GLN ARG TRP LEU VAL THR SER GLU GLY SEQRES 17 A 311 ALA PHE SER TYR LEU ALA LYS ASP TYR GLY PHE LYS GLU SEQRES 18 A 311 VAL TYR LEU TRP PRO ILE ASN ALA GLU GLN GLN GLY ILE SEQRES 19 A 311 PRO GLN GLN VAL ARG HIS VAL ILE ASP ILE ILE ARG GLU SEQRES 20 A 311 ASN LYS ILE PRO VAL VAL PHE SER GLU SER THR ILE SER SEQRES 21 A 311 ASP LYS PRO ALA LYS GLN VAL SER LYS GLU THR GLY ALA SEQRES 22 A 311 GLN TYR GLY GLY VAL LEU TYR VAL ASP SER LEU SER GLY SEQRES 23 A 311 GLU LYS GLY PRO VAL PRO THR TYR ILE SER LEU ILE ASN SEQRES 24 A 311 MET THR VAL ASP THR ILE ALA LYS GLY PHE GLY GLN FORMUL 2 HOH *166(H2 O) HELIX 1 AA1 PHE A 48 GLY A 60 1 13 HELIX 2 AA2 THR A 81 SER A 90 1 10 HELIX 3 AA3 TRP A 104 SER A 111 1 8 HELIX 4 AA4 HIS A 141 MET A 144 5 4 HELIX 5 AA5 SER A 145 ASP A 164 1 20 HELIX 6 AA6 HIS A 167 ALA A 184 1 18 HELIX 7 AA7 LEU A 185 SER A 194 1 10 HELIX 8 AA8 ARG A 195 ILE A 196 5 2 HELIX 9 AA9 PRO A 197 GLN A 200 5 4 HELIX 10 AB1 PHE A 210 GLY A 218 1 9 HELIX 11 AB2 HIS A 240 LYS A 249 1 10 HELIX 12 AB3 ASP A 261 GLY A 272 1 12 HELIX 13 AB4 THR A 293 PHE A 309 1 17 SHEET 1 AA1 4 ALA A 63 SER A 67 0 SHEET 2 AA1 4 PHE A 42 THR A 46 1 N VAL A 44 O VAL A 64 SHEET 3 AA1 4 LEU A 93 TRP A 96 1 O LEU A 95 N VAL A 45 SHEET 4 AA1 4 SER A 117 VAL A 119 1 O ALA A 118 N ILE A 94 SHEET 1 AA2 2 TRP A 202 THR A 205 0 SHEET 2 AA2 2 LYS A 220 TYR A 223 1 O LYS A 220 N LEU A 203 SHEET 1 AA3 2 VAL A 252 GLU A 256 0 SHEET 2 AA3 2 GLN A 274 LEU A 279 1 O GLY A 277 N SER A 255 CRYST1 40.017 52.426 113.263 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 0.024989 0.000000 0.000000 0.00000 SCALE2 0.000000 0.019075 0.000000 0.00000 SCALE3 0.000000 0.000000 0.008829 0.00000