HEADER TRANSPORT PROTEIN 13-MAR-24 9B1U TITLE CRYSTAL STRUCTURE OF PQQT WITH PQQ BOUND COMPND MOL_ID: 1; COMPND 2 MOLECULE: PUTATIVE ABC TRANSPORTER PERIPLASMIC SOLUTE-BINDING COMPND 3 PROTEIN; COMPND 4 CHAIN: A; COMPND 5 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: METHYLORUBRUM EXTORQUENS (STRAIN CM4 / NCIMB SOURCE 3 13688); SOURCE 4 ORGANISM_TAXID: 408; SOURCE 5 STRAIN: CM4 / NCIMB 13688; SOURCE 6 GENE: MCHL_2142; SOURCE 7 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 8 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS PERIPLASMIC BINDING PROTEIN, TRANSPORT PROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR D.BOGGS,A.BRUCHS,P.THOMPSON,L.OLSHANSKY,J.BRIDWELL-RABB REVDAT 1 21-AUG-24 9B1U 0 JRNL AUTH P.J.THOMPSON,D.G.BOGGS,C.A.WILSON,A.T.BRUCHS,U.VELIDANDLA, JRNL AUTH 2 J.BRIDWELL-RABB,L.OLSHANSKY JRNL TITL STRUCTURE-DRIVEN DEVELOPMENT OF A BIOMIMETIC RARE EARTH JRNL TITL 2 ARTIFICIAL METALLOPROTEIN. JRNL REF PROC.NATL.ACAD.SCI.USA V. 121 36121 2024 JRNL REFN ESSN 1091-6490 JRNL PMID 39116128 JRNL DOI 10.1073/PNAS.2405836121 REMARK 2 REMARK 2 RESOLUTION. 1.46 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.21-5207 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) : 1.46 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 37.92 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.350 REMARK 3 COMPLETENESS FOR RANGE (%) : 94.9 REMARK 3 NUMBER OF REFLECTIONS : 42757 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.199 REMARK 3 R VALUE (WORKING SET) : 0.199 REMARK 3 FREE R VALUE : 0.207 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.000 REMARK 3 FREE R VALUE TEST SET COUNT : 2139 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 37.9200 - 3.6000 0.99 3049 161 0.1813 0.1908 REMARK 3 2 3.6000 - 2.8600 1.00 2901 153 0.1846 0.1722 REMARK 3 3 2.8600 - 2.5000 0.98 2846 149 0.1958 0.2141 REMARK 3 4 2.5000 - 2.2700 1.00 2881 152 0.2016 0.2130 REMARK 3 5 2.2700 - 2.1100 1.00 2825 149 0.2028 0.2098 REMARK 3 6 2.1100 - 1.9800 1.00 2854 150 0.2133 0.2165 REMARK 3 7 1.9800 - 1.8800 0.98 2764 145 0.2122 0.2197 REMARK 3 8 1.8800 - 1.8000 0.99 2814 149 0.2152 0.2856 REMARK 3 9 1.8000 - 1.7300 1.00 2814 148 0.2163 0.2426 REMARK 3 10 1.7300 - 1.6700 1.00 2784 146 0.2310 0.2345 REMARK 3 11 1.6700 - 1.6200 1.00 2847 151 0.2349 0.2325 REMARK 3 12 1.6200 - 1.5700 0.99 2781 147 0.2260 0.2586 REMARK 3 13 1.5700 - 1.5300 0.87 2437 128 0.2393 0.2687 REMARK 3 14 1.5300 - 1.4900 0.76 2139 112 0.2427 0.2499 REMARK 3 15 1.4900 - 1.4600 0.67 1882 99 0.2699 0.2750 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) : 0.156 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 22.327 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 19.46 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 27.21 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 : 0.014 2519 REMARK 3 ANGLE : 1.589 3435 REMARK 3 CHIRALITY : 0.091 377 REMARK 3 PLANARITY : 0.020 459 REMARK 3 DIHEDRAL : 12.113 916 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 9B1U COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 15-MAR-24. REMARK 100 THE DEPOSITION ID IS D_1000282463. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 23-AUG-23 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 : SSRL REMARK 200 BEAMLINE : BL12-2 REMARK 200 X-RAY GENERATOR MODEL : NULL 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 : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS EIGER X 16M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS 20230630 REMARK 200 DATA SCALING SOFTWARE : XDS 20230630 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 42803 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.460 REMARK 200 RESOLUTION RANGE LOW (A) : 40.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 94.9 REMARK 200 DATA REDUNDANCY : 12.53 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 26.5700 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.46 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.55 REMARK 200 COMPLETENESS FOR SHELL (%) : 73.8 REMARK 200 DATA REDUNDANCY IN SHELL : 9.37 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 1.21-5207 REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 36.32 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 1.93 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 20 MM NACL, 20 MM HEPES PH 7.5, 100 MM REMARK 280 CITRIC ACID PH 3.8, AND 3.0 M NACL, VAPOR DIFFUSION, SITTING REMARK 280 DROP, TEMPERATURE 291K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 2 21 21 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+1/2,-Z+1/2 REMARK 290 4555 -X,-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 26.59550 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 59.53400 REMARK 290 SMTRY1 4 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 26.59550 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 59.53400 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 ALA A 28 REMARK 465 ALA A 327 REMARK 465 SER A 328 REMARK 465 GLY A 329 REMARK 465 ASN A 330 REMARK 465 GLY A 331 REMARK 465 HIS A 332 REMARK 465 HIS A 333 REMARK 465 HIS A 334 REMARK 465 HIS A 335 REMARK 465 HIS A 336 REMARK 465 HIS A 337 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 ASP A 305 39.74 -71.85 REMARK 500 ARG A 306 -112.08 -137.26 REMARK 500 LEU A 307 71.72 53.50 REMARK 500 LEU A 307 41.25 -102.74 REMARK 500 ALA A 308 86.89 57.23 REMARK 500 ALA A 310 -116.58 -121.23 REMARK 500 GLN A 311 62.59 38.23 REMARK 500 REMARK 500 REMARK: NULL DBREF 9B1U A 28 331 UNP B7KXB5 B7KXB5_METC4 28 331 SEQADV 9B1U ALA A 192 UNP B7KXB5 CYS 192 CONFLICT SEQADV 9B1U HIS A 332 UNP B7KXB5 EXPRESSION TAG SEQADV 9B1U HIS A 333 UNP B7KXB5 EXPRESSION TAG SEQADV 9B1U HIS A 334 UNP B7KXB5 EXPRESSION TAG SEQADV 9B1U HIS A 335 UNP B7KXB5 EXPRESSION TAG SEQADV 9B1U HIS A 336 UNP B7KXB5 EXPRESSION TAG SEQADV 9B1U HIS A 337 UNP B7KXB5 EXPRESSION TAG SEQRES 1 A 310 ALA GLY GLU THR PHE ARG LEU GLY VAL LEU PRO PHE GLY SEQRES 2 A 310 THR ALA SER TRP GLU ALA ALA VAL ILE LYS ALA ARG GLY SEQRES 3 A 310 PHE ASP THR ALA ASN GLY PHE THR LEU ASP ILE VAL LYS SEQRES 4 A 310 LEU ALA GLY ASN ASP ALA ALA ARG ILE ALA PHE LEU GLY SEQRES 5 A 310 GLY GLN VAL ASP ALA ILE VAL GLY ASP LEU ILE PHE ALA SEQRES 6 A 310 ALA ARG LEU GLY ASN GLU GLY ARG GLY VAL ARG PHE SER SEQRES 7 A 310 PRO TYR SER THR THR GLU GLY ALA LEU MET VAL PRO ALA SEQRES 8 A 310 GLY SER PRO ILE THR ASP LEU LYS GLY LEU ALA GLY LYS SEQRES 9 A 310 ARG LEU GLY VAL ALA GLY GLY ALA LEU ASP LYS ASN TRP SEQRES 10 A 310 ILE LEU LEU ARG ALA GLN ALA ARG GLU THR ALA GLY LEU SEQRES 11 A 310 GLU LEU GLU ASN VAL ALA GLN ILE ALA TYR GLY ALA PRO SEQRES 12 A 310 PRO LEU LEU ALA GLN LYS LEU GLU THR GLY GLU LEU ASP SEQRES 13 A 310 ALA ALA LEU LEU TYR TRP GLN PHE ALA ALA ARG LEU GLU SEQRES 14 A 310 ALA LYS GLY PHE LYS ARG LEU ILE SER ALA ASP ASP VAL SEQRES 15 A 310 MET ARG ALA PHE GLY ALA LYS GLY ALA VAL SER LEU ILE SEQRES 16 A 310 GLY TYR LEU TYR GLU GLY HIS THR VAL ALA ASP ARG GLY SEQRES 17 A 310 GLU VAL VAL ARG GLY PHE ALA ARG ALA SER ALA ALA ALA SEQRES 18 A 310 LYS ASP ALA LEU ALA ASN GLU PRO ALA LEU TRP GLU THR SEQRES 19 A 310 VAL ARG PRO LEU MET ALA ALA GLU ASP ASP ALA THR PHE SEQRES 20 A 310 ALA THR LEU LYS ARG ASP PHE LEU ALA GLY ILE PRO ARG SEQRES 21 A 310 ARG PRO ILE ALA ALA GLU ARG ALA ASP GLY GLU ARG ILE SEQRES 22 A 310 TYR ALA ALA LEU ASP ARG LEU ALA GLY ALA GLN LEU LEU SEQRES 23 A 310 GLY VAL GLY LYS SER LEU PRO PRO ASP LEU TYR LEU ASP SEQRES 24 A 310 ALA SER GLY ASN GLY HIS HIS HIS HIS HIS HIS HET PQQ A 401 24 HET NA A 402 1 HET NA A 403 1 HETNAM PQQ PYRROLOQUINOLINE QUINONE HETNAM NA SODIUM ION FORMUL 2 PQQ C14 H6 N2 O8 FORMUL 3 NA 2(NA 1+) FORMUL 5 HOH *246(H2 O) HELIX 1 AA1 THR A 41 ARG A 52 1 12 HELIX 2 AA2 ASP A 55 GLY A 59 5 5 HELIX 3 AA3 GLY A 69 GLY A 79 1 11 HELIX 4 AA4 LEU A 89 GLU A 98 1 10 HELIX 5 AA5 ASP A 124 ALA A 129 5 6 HELIX 6 AA6 ASP A 141 GLY A 156 1 16 HELIX 7 AA7 GLU A 158 ALA A 163 1 6 HELIX 8 AA8 ALA A 169 THR A 179 1 11 HELIX 9 AA9 TRP A 189 ALA A 197 1 9 HELIX 10 AB1 SER A 205 GLY A 214 1 10 HELIX 11 AB2 GLU A 227 ARG A 234 1 8 HELIX 12 AB3 ARG A 234 GLU A 255 1 22 HELIX 13 AB4 GLU A 255 ARG A 263 1 9 HELIX 14 AB5 PRO A 264 ALA A 267 5 4 HELIX 15 AB6 ASP A 270 ILE A 285 1 16 HELIX 16 AB7 PRO A 289 ASP A 305 1 17 SHEET 1 AA1 2 THR A 31 VAL A 36 0 SHEET 2 AA1 2 THR A 61 LYS A 66 1 O ASP A 63 N PHE A 32 SHEET 1 AA2 3 ALA A 84 ASP A 88 0 SHEET 2 AA2 3 ILE A 222 TYR A 226 -1 O GLY A 223 N GLY A 87 SHEET 3 AA2 3 ARG A 103 SER A 108 -1 N ARG A 103 O TYR A 226 SHEET 1 AA3 5 GLN A 164 GLY A 168 0 SHEET 2 AA3 5 ARG A 132 ALA A 136 1 N LEU A 133 O ALA A 166 SHEET 3 AA3 5 ALA A 184 LEU A 187 1 O LEU A 186 N GLY A 134 SHEET 4 AA3 5 ALA A 113 PRO A 117 -1 N ALA A 113 O LEU A 187 SHEET 5 AA3 5 PHE A 200 ILE A 204 -1 O LYS A 201 N VAL A 116 LINK NA NA A 402 O HOH A 581 1555 1555 3.12 CRYST1 40.004 53.191 119.068 90.00 90.00 90.00 P 2 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 0.024998 0.000000 0.000000 0.00000 SCALE2 0.000000 0.018800 0.000000 0.00000 SCALE3 0.000000 0.000000 0.008399 0.00000