HEADER TRANSPORT PROTEIN 30-MAR-20 6WCE TITLE STRUCTURE OF THE PERIPLASMIC BINDING PROTEIN P5PA COMPND MOL_ID: 1; COMPND 2 MOLECULE: PYRIDOXAL-5-PHOSPHATE BINDING PROTEIN A (P5PA); COMPND 3 CHAIN: A; COMPND 4 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: ACTINOBACILLUS PLEUROPNEUMONIAE; SOURCE 3 ORGANISM_TAXID: 715; SOURCE 4 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21(DE3); SOURCE 5 EXPRESSION_SYSTEM_TAXID: 469008 KEYWDS TYPE-II PERIPLASMIC BINDING PROTEIN, VITAMINB6, NUTRITION, TRANSPORT KEYWDS 2 PROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR C.PAN,A.ZIMMER,M.SHAH,M.HUYNH,C.C.L.LAI,B.SIT,Y.HOODA,T.F.MORAES REVDAT 3 18-OCT-23 6WCE 1 REMARK REVDAT 2 22-SEP-21 6WCE 1 JRNL REVDAT 1 25-AUG-21 6WCE 0 JRNL AUTH C.PAN,A.ZIMMER,M.SHAH,M.S.HUYNH,C.C.LAI,B.SIT,Y.HOODA, JRNL AUTH 2 D.M.CURRAN,T.F.MORAES JRNL TITL ACTINOBACILLUS UTILIZES A BINDING PROTEIN-DEPENDENT ABC JRNL TITL 2 TRANSPORTER TO ACQUIRE THE ACTIVE FORM OF VITAMIN B 6 . JRNL REF J.BIOL.CHEM. V. 297 01046 2021 JRNL REFN ESSN 1083-351X JRNL PMID 34358566 JRNL DOI 10.1016/J.JBC.2021.101046 REMARK 2 REMARK 2 RESOLUTION. 1.75 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.13_2998 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 REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.75 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 66.62 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.370 REMARK 3 COMPLETENESS FOR RANGE (%) : 92.8 REMARK 3 NUMBER OF REFLECTIONS : 26906 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.162 REMARK 3 R VALUE (WORKING SET) : 0.161 REMARK 3 FREE R VALUE : 0.195 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.030 REMARK 3 FREE R VALUE TEST SET COUNT : 1353 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 66.6200 - 3.7800 0.97 2766 146 0.1373 0.1556 REMARK 3 2 3.7800 - 3.0000 0.98 2683 151 0.1625 0.1856 REMARK 3 3 3.0000 - 2.6200 0.98 2716 139 0.1777 0.2014 REMARK 3 4 2.6200 - 2.3800 0.98 2648 153 0.1693 0.1980 REMARK 3 5 2.3800 - 2.2100 0.97 2696 139 0.1613 0.1937 REMARK 3 6 2.2100 - 2.0800 0.97 2647 128 0.1503 0.1934 REMARK 3 7 2.0800 - 1.9800 0.97 2644 145 0.1562 0.2225 REMARK 3 8 1.9800 - 1.8900 0.96 2633 132 0.1583 0.1997 REMARK 3 9 1.8900 - 1.8200 0.92 2529 136 0.1736 0.2382 REMARK 3 10 1.8200 - 1.7540 0.59 1591 84 0.2112 0.2817 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) : 0.170 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 18.852 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 7.94 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 9.54 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 2519 REMARK 3 ANGLE : 0.787 3403 REMARK 3 CHIRALITY : 0.272 372 REMARK 3 PLANARITY : 0.005 438 REMARK 3 DIHEDRAL : 15.732 952 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 6WCE COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 31-MAR-20. REMARK 100 THE DEPOSITION ID IS D_1000247789. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 23-AUG-14 REMARK 200 TEMPERATURE (KELVIN) : 105 REMARK 200 PH : 7 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : APS REMARK 200 BEAMLINE : 24-ID-E REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.97918 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 315 REMARK 200 INTENSITY-INTEGRATION SOFTWARE : IMOSFLM REMARK 200 DATA SCALING SOFTWARE : XSCALE REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 28927 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.750 REMARK 200 RESOLUTION RANGE LOW (A) : 66.624 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 92.8 REMARK 200 DATA REDUNDANCY : 5.100 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 24.6800 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.75 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.82 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: 4R73 REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 33.54 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 1.85 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.05M POTASSIUM THIOCYANATE, 27.5% PEG REMARK 280 MME 2000, PH 7, VAPOR DIFFUSION, SITTING DROP, TEMPERATURE REMARK 280 294.15K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 1 21 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,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 21.13650 REMARK 290 SMTRY3 2 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 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 -37 REMARK 465 LYS A -36 REMARK 465 TYR A -35 REMARK 465 LEU A -34 REMARK 465 LEU A -33 REMARK 465 PRO A -32 REMARK 465 THR A -31 REMARK 465 ALA A -30 REMARK 465 ALA A -29 REMARK 465 ALA A -28 REMARK 465 GLY A -27 REMARK 465 LEU A -26 REMARK 465 LEU A -25 REMARK 465 LEU A -24 REMARK 465 LEU A -23 REMARK 465 ALA A -22 REMARK 465 ALA A -21 REMARK 465 GLN A -20 REMARK 465 PRO A -19 REMARK 465 ALA A -18 REMARK 465 MET A -17 REMARK 465 ALA A -16 REMARK 465 MET A -15 REMARK 465 ALA A -14 REMARK 465 HIS A -13 REMARK 465 HIS A -12 REMARK 465 HIS A -11 REMARK 465 HIS A -10 REMARK 465 HIS A -9 REMARK 465 HIS A -8 REMARK 465 LEU A -7 REMARK 465 VAL A -6 REMARK 465 PRO A -5 REMARK 465 ARG A -4 REMARK 465 GLY A -3 REMARK 465 SER A -2 REMARK 465 ALA A -1 REMARK 465 ALA A 0 REMARK 465 LEU A 315 REMARK 465 ALA A 316 REMARK 465 LYS A 317 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 ASN A 50 75.92 -157.02 REMARK 500 ILE A 313 -61.67 -99.06 REMARK 500 REMARK 500 REMARK: NULL DBREF 6WCE A -37 317 PDB 6WCE 6WCE -37 317 SEQRES 1 A 355 MET LYS TYR LEU LEU PRO THR ALA ALA ALA GLY LEU LEU SEQRES 2 A 355 LEU LEU ALA ALA GLN PRO ALA MET ALA MET ALA HIS HIS SEQRES 3 A 355 HIS HIS HIS HIS LEU VAL PRO ARG GLY SER ALA ALA GLU SEQRES 4 A 355 GLY ARG LEU THR VAL TYR CYS THR VAL GLN ASN GLU VAL SEQRES 5 A 355 CYS GLU ASN LEU THR GLN LYS PHE ALA LYS GLN TYR GLN SEQRES 6 A 355 VAL GLU THR GLN PHE ILE GLN GLY GLY THR GLY THR ILE SEQRES 7 A 355 PHE GLY LYS ILE LYS ALA GLU LYS ASP ASN PRO GLN ALA SEQRES 8 A 355 ASP ILE TRP VAL GLY GLY THR ILE GLU PRO HIS PHE GLN SEQRES 9 A 355 ALA GLY GLU LEU GLY LEU LEU GLU SER TYR ARG SER PRO SEQRES 10 A 355 LYS GLN ALA GLU ILE LEU PRO GLN PHE LYS SER LEU MET SEQRES 11 A 355 GLU LYS ARG GLY ASP LYS THR SER ILE ILE TYR MET LEU SEQRES 12 A 355 VAL LEU GLY PHE GLY VAL ASN SER GLU LYS LEU GLN LYS SEQRES 13 A 355 LEU GLY VAL LYS ALA PRO GLN SER TRP ASP ASP LEU LEU SEQRES 14 A 355 ASN PRO ALA PHE LYS GLY GLU ILE GLN LEU PRO ASP PRO SEQRES 15 A 355 ARG SER SER GLY THR THR TYR THR ILE MET ALA THR LEU SEQRES 16 A 355 ILE GLN LYS LEU GLY GLU GLU LYS ALA PHE GLU TYR LEU SEQRES 17 A 355 LYS LYS LEU ASN GLU ASN VAL SER GLN TYR VAL LYS SER SEQRES 18 A 355 ASN LEU VAL THR ALA ASN LEU SER ARG GLY GLU SER SER SEQRES 19 A 355 ALA SER ILE GLY PHE VAL HIS ALA TYR ALA THR GLU LYS SEQRES 20 A 355 GLU LYS GLY ALA PRO VAL GLU THR VAL ILE PRO ALA GLY SEQRES 21 A 355 LYS VAL GLY TYR ALA LEU GLY GLY ALA SER ILE ILE LYS SEQRES 22 A 355 ASN ALA ARG ASN LEU GLU ASN ALA LYS LEU PHE MET ASP SEQRES 23 A 355 TYR VAL LEU SER ALA GLU THR GLN GLU LEU PRO TRP ARG SEQRES 24 A 355 GLU HIS GLY VAL TYR GLN ILE PRO THR ASN ALA ASN ALA SEQRES 25 A 355 LYS ALA SER PRO SER SER VAL ASP PRO LYS LYS LEU ASP SEQRES 26 A 355 LEU LEU ASP PHE ASP PHE ASP LYS PHE GLY SER SER GLU SEQRES 27 A 355 GLU GLY LYS ARG LEU ILE ASP LYS TRP LEU THR GLU ILE SEQRES 28 A 355 LYS LEU ALA LYS HET PLP A 401 24 HETNAM PLP PYRIDOXAL-5'-PHOSPHATE HETSYN PLP VITAMIN B6 PHOSPHATE FORMUL 2 PLP C8 H10 N O6 P FORMUL 3 HOH *241(H2 O) HELIX 1 AA1 GLN A 11 GLN A 27 1 17 HELIX 2 AA2 GLY A 36 GLU A 47 1 12 HELIX 3 AA3 ILE A 61 LEU A 70 1 10 HELIX 4 AA4 SER A 78 ILE A 84 5 7 HELIX 5 AA5 LEU A 85 GLN A 87 5 3 HELIX 6 AA6 PHE A 88 GLY A 96 1 9 HELIX 7 AA7 SER A 113 GLY A 120 1 8 HELIX 8 AA8 TRP A 127 LYS A 136 5 10 HELIX 9 AA9 SER A 147 GLY A 162 1 16 HELIX 10 AB1 GLY A 162 GLU A 175 1 14 HELIX 11 AB2 LYS A 182 ARG A 192 1 11 HELIX 12 AB3 VAL A 202 LYS A 211 1 10 HELIX 13 AB4 ASN A 239 LEU A 251 1 13 HELIX 14 AB5 SER A 252 GLY A 264 1 13 HELIX 15 AB6 ASP A 282 LEU A 286 5 5 HELIX 16 AB7 ASP A 292 GLY A 297 1 6 HELIX 17 AB8 SER A 298 ILE A 313 1 16 SHEET 1 AA1 6 VAL A 28 GLN A 34 0 SHEET 2 AA1 6 GLY A 2 CYS A 8 1 N CYS A 8 O ILE A 33 SHEET 3 AA1 6 ILE A 55 THR A 60 1 O VAL A 57 N TYR A 7 SHEET 4 AA1 6 TYR A 226 ILE A 233 -1 O SER A 232 N TRP A 56 SHEET 5 AA1 6 SER A 100 ASN A 112 -1 N LEU A 105 O ALA A 227 SHEET 6 AA1 6 VAL A 215 VAL A 218 -1 O VAL A 218 N PHE A 109 SHEET 1 AA2 5 VAL A 177 VAL A 181 0 SHEET 2 AA2 5 ILE A 139 PRO A 142 1 N ILE A 139 O SER A 178 SHEET 3 AA2 5 ALA A 197 PHE A 201 1 O ALA A 197 N GLN A 140 SHEET 4 AA2 5 SER A 100 ASN A 112 -1 N GLY A 108 O GLY A 200 SHEET 5 AA2 5 ILE A 268 PRO A 269 -1 O ILE A 268 N MET A 104 SSBOND 1 CYS A 8 CYS A 15 1555 1555 2.04 CRYST1 51.468 42.273 69.601 90.00 106.82 90.00 P 1 21 1 2 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 0.019430 0.000000 0.005873 0.00000 SCALE2 0.000000 0.023656 0.000000 0.00000 SCALE3 0.000000 0.000000 0.015010 0.00000