HEADER TRANSPORT PROTEIN 22-SEP-23 8WGK TITLE CRYSTAL STRUCTURE OF RHODOTHERMUS MARINUS SUBSTRATE-BINDING PROTEIN TITLE 2 (BR SOAKING) COMPND MOL_ID: 1; COMPND 2 MOLECULE: ABC-TYPE UNCHARACTERIZED TRANSPORT SYSTEM PERIPLASMIC COMPND 3 COMPONENT-LIKE PROTEIN; COMPND 4 CHAIN: A; COMPND 5 SYNONYM: SINGLE DOMAIN SUBSTRATE BINDING PROTEIN; COMPND 6 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: RHODOTHERMUS MARINUS DSM 4252; SOURCE 3 ORGANISM_TAXID: 518766; SOURCE 4 GENE: RMAR_2176; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21(DE3); SOURCE 6 EXPRESSION_SYSTEM_TAXID: 469008 KEYWDS SUBSTRATE BINDING PROTEIN, TRANSPORT PROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR K.H.NAM REVDAT 2 17-APR-24 8WGK 1 JRNL REVDAT 1 04-OCT-23 8WGK 0 JRNL AUTH K.H.NAM JRNL TITL STRUCTURAL AND BIOINFORMATICS ANALYSIS OF SINGLE-DOMAIN JRNL TITL 2 SUBSTRATE-BINDING PROTEIN FROM RHODOTHERMUS MARINUS. JRNL REF BIOCHEM BIOPHYS REP V. 37 01611 2024 JRNL REFN ESSN 2405-5808 JRNL PMID 38269326 JRNL DOI 10.1016/J.BBREP.2023.101611 REMARK 2 REMARK 2 RESOLUTION. 1.75 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) : 1.75 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 21.87 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.340 REMARK 3 COMPLETENESS FOR RANGE (%) : 97.5 REMARK 3 NUMBER OF REFLECTIONS : 13384 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.226 REMARK 3 R VALUE (WORKING SET) : 0.222 REMARK 3 FREE R VALUE : 0.261 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 10.020 REMARK 3 FREE R VALUE TEST SET COUNT : 1341 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 21.8700 - 3.7700 0.82 1090 119 0.2375 0.2776 REMARK 3 2 3.7600 - 2.9900 0.98 1229 141 0.2163 0.2637 REMARK 3 3 2.9900 - 2.6100 0.99 1219 137 0.2289 0.2488 REMARK 3 4 2.6100 - 2.3700 0.99 1231 132 0.2260 0.2568 REMARK 3 5 2.3700 - 2.2000 0.99 1216 135 0.2140 0.2521 REMARK 3 6 2.2000 - 2.0700 1.00 1225 142 0.2030 0.2718 REMARK 3 7 2.0700 - 1.9700 1.00 1200 132 0.2096 0.2480 REMARK 3 8 1.9700 - 1.8900 1.00 1210 136 0.2089 0.2394 REMARK 3 9 1.8900 - 1.8100 1.00 1210 134 0.2210 0.2618 REMARK 3 10 1.8100 - 1.7500 1.00 1213 133 0.2254 0.2406 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) : 0.170 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 22.590 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL 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 : 0.006 1077 REMARK 3 ANGLE : 0.838 1460 REMARK 3 CHIRALITY : 0.055 175 REMARK 3 PLANARITY : 0.008 182 REMARK 3 DIHEDRAL : 5.932 143 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 8WGK COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 22-SEP-23. REMARK 100 THE DEPOSITION ID IS D_1300041223. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 25-NOV-16 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 7.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : PAL/PLS REMARK 200 BEAMLINE : 7A (6B, 6C1) REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 270 REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : HKL-2000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 13670 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.750 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 (%) : 97.4 REMARK 200 DATA REDUNDANCY : 3.800 REMARK 200 R MERGE (I) : 0.06400 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 36.4700 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) : 1.78 REMARK 200 COMPLETENESS FOR SHELL (%) : NULL REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : 0.35500 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: MOLREP REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 23.21 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 1.60 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: HEPES , POLYETHYLENE GLYCOL 3,350, PH REMARK 280 7.5, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 295K 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 23.11550 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 28.75900 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 24.56450 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 28.75900 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 23.11550 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 24.56450 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 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 HIS A 2 REMARK 465 THR A 3 REMARK 465 LEU A 4 REMARK 465 ARG A 5 REMARK 465 LEU A 6 REMARK 465 PHE A 7 REMARK 465 THR A 8 REMARK 465 VAL A 9 REMARK 465 LEU A 10 REMARK 465 SER A 11 REMARK 465 LEU A 12 REMARK 465 LEU A 13 REMARK 465 LEU A 14 REMARK 465 THR A 15 REMARK 465 SER A 16 REMARK 465 ALA A 17 REMARK 465 PHE A 18 REMARK 465 THR A 19 REMARK 465 LEU A 20 REMARK 465 PHE A 21 REMARK 465 PRO A 22 REMARK 465 GLU A 23 REMARK 465 THR A 24 REMARK 465 GLU A 25 REMARK 465 THR A 26 REMARK 465 ARG A 58 REMARK 465 ASP A 59 REMARK 465 GLU A 60 REMARK 465 VAL A 61 REMARK 465 LEU A 62 REMARK 465 PRO A 63 REMARK 465 GLN A 64 REMARK 465 ASP A 151 REMARK 465 ALA A 152 REMARK 465 GLU A 153 REMARK 465 GLY A 154 REMARK 465 GLN A 176 REMARK 465 ASP A 177 REMARK 465 ARG A 178 REMARK 465 THR A 179 REMARK 465 ALA A 180 REMARK 465 PHE A 181 REMARK 465 LEU A 182 REMARK 465 ALA A 183 REMARK 465 MET A 184 REMARK 465 ASN A 185 REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CLOSE CONTACTS IN SAME ASYMMETRIC UNIT REMARK 500 REMARK 500 THE FOLLOWING ATOMS ARE IN CLOSE CONTACT. REMARK 500 REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI DISTANCE REMARK 500 OE1 GLU A 137 O HOH A 201 2.10 REMARK 500 NH2 ARG A 92 O HOH A 202 2.14 REMARK 500 O GLU A 80 O HOH A 203 2.17 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CLOSE CONTACTS REMARK 500 REMARK 500 THE FOLLOWING ATOMS THAT ARE RELATED BY CRYSTALLOGRAPHIC REMARK 500 SYMMETRY ARE IN CLOSE CONTACT. AN ATOM LOCATED WITHIN 0.15 REMARK 500 ANGSTROMS OF A SYMMETRY RELATED ATOM IS ASSUMED TO BE ON A REMARK 500 SPECIAL POSITION AND IS, THEREFORE, LISTED IN REMARK 375 REMARK 500 INSTEAD OF REMARK 500. ATOMS WITH NON-BLANK ALTERNATE REMARK 500 LOCATION INDICATORS ARE NOT INCLUDED IN THE CALCULATIONS. REMARK 500 REMARK 500 DISTANCE CUTOFF: REMARK 500 2.2 ANGSTROMS FOR CONTACTS NOT INVOLVING HYDROGEN ATOMS REMARK 500 1.6 ANGSTROMS FOR CONTACTS INVOLVING HYDROGEN ATOMS REMARK 500 REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI SSYMOP DISTANCE REMARK 500 OE2 GLU A 39 NH1 ARG A 96 2554 2.18 REMARK 500 REMARK 500 REMARK: NULL 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 GLU A 108 38.70 -150.33 REMARK 500 REMARK 500 REMARK: NULL DBREF 8WGK A 1 185 UNP D0MDR1 D0MDR1_RHOM4 1 185 SEQRES 1 A 185 MET HIS THR LEU ARG LEU PHE THR VAL LEU SER LEU LEU SEQRES 2 A 185 LEU THR SER ALA PHE THR LEU PHE PRO GLU THR GLU THR SEQRES 3 A 185 GLU VAL THR PRO ILE GLN GLN LEU PHE LEU ILE LYS GLU SEQRES 4 A 185 LEU LYS PRO GLY ILE ALA ARG ILE GLY VAL ILE TRP ASP SEQRES 5 A 185 LYS ASN ALA ALA ASN ARG ASP GLU VAL LEU PRO GLN LEU SEQRES 6 A 185 GLN ARG ALA SER ALA ALA THR GLY ILE LYS VAL VAL VAL SEQRES 7 A 185 ALA GLU VAL ALA SER LEU GLN GLU VAL ALA PRO GLN PHE SEQRES 8 A 185 ARG THR LEU LEU ARG ASP HIS GLN VAL GLU ALA LEU TRP SEQRES 9 A 185 VAL LEU GLU GLU SER GLY LEU LEU GLY GLN ALA ALA ALA SEQRES 10 A 185 ARG SER PHE LEU ILE LYS ASN ALA THR GLN ALA GLY MET SEQRES 11 A 185 PRO VAL PHE ALA PRO SER GLU THR TRP LEU LYS GLU GLY SEQRES 12 A 185 ALA CYS VAL THR TRP ARG LYS ASP ALA GLU GLY ILE ARG SEQRES 13 A 185 LEU VAL VAL ASN LYS ALA VAL ALA GLU ALA MET GLY ILE SEQRES 14 A 185 THR ILE PRO ALA LYS TYR GLN ASP ARG THR ALA PHE LEU SEQRES 15 A 185 ALA MET ASN FORMUL 2 HOH *51(H2 O) HELIX 1 AA1 THR A 29 LYS A 41 1 13 HELIX 2 AA2 GLN A 66 GLY A 73 1 8 HELIX 3 AA3 SER A 83 GLN A 85 5 3 HELIX 4 AA4 GLU A 86 GLN A 99 1 14 HELIX 5 AA5 GLY A 110 GLY A 113 5 4 HELIX 6 AA6 GLN A 114 ALA A 128 1 15 HELIX 7 AA7 SER A 136 GLU A 142 1 7 HELIX 8 AA8 ASN A 160 MET A 167 1 8 SHEET 1 AA1 4 LYS A 75 VAL A 81 0 SHEET 2 AA1 4 ARG A 46 ASP A 52 1 N VAL A 49 O VAL A 77 SHEET 3 AA1 4 LEU A 103 TRP A 104 1 O TRP A 104 N GLY A 48 SHEET 4 AA1 4 VAL A 132 PHE A 133 1 O PHE A 133 N LEU A 103 SHEET 1 AA2 2 VAL A 146 ARG A 149 0 SHEET 2 AA2 2 ARG A 156 VAL A 159 -1 O ARG A 156 N ARG A 149 CRYST1 46.231 49.129 57.518 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 0.021631 0.000000 0.000000 0.00000 SCALE2 0.000000 0.020355 0.000000 0.00000 SCALE3 0.000000 0.000000 0.017386 0.00000