HEADER UNKNOWN FUNCTION 22-APR-19 6ONP TITLE CRYSTAL STRUCTURE OF PERIPLASMIC BINDING PROTEIN XOXJ FROM TITLE 2 METHYLOBACTERIUM EXTORQUENS AM1 COMPND MOL_ID: 1; COMPND 2 MOLECULE: PERIPLASMIC BINDING PROTEIN XOXJ; COMPND 3 CHAIN: A; COMPND 4 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: METHYLOBACTERIUM EXTORQUENS (STRAIN ATCC 14718 SOURCE 3 / DSM 1338 / JCM 2805 / NCIMB 9133 / AM1); SOURCE 4 ORGANISM_TAXID: 272630; SOURCE 5 STRAIN: ATCC 14718 / DSM 1338 / JCM 2805 / NCIMB 9133 / AM1; SOURCE 6 GENE: XOXJ, MEXAM1_META1P1742; SOURCE 7 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21(DE3); SOURCE 8 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 9 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 10 EXPRESSION_SYSTEM_PLASMID: PET24A KEYWDS PERISPLASMIC BINDING PROTEIN, SOLUTE-BINDING PROTEIN, METHANOL KEYWDS 2 DEHYDROGENASE, UNKNOWN FUNCTION EXPDTA X-RAY DIFFRACTION AUTHOR H.R.ROSE,E.M.TAYLOR,A.K.BOAL REVDAT 5 01-JAN-20 6ONP 1 REMARK REVDAT 4 02-OCT-19 6ONP 1 JRNL REVDAT 3 21-AUG-19 6ONP 1 JRNL REVDAT 2 17-JUL-19 6ONP 1 REMARK REVDAT 1 08-MAY-19 6ONP 0 JRNL AUTH E.R.FEATHERSTON,H.R.ROSE,M.J.MCBRIDE,E.M.TAYLOR,A.K.BOAL, JRNL AUTH 2 J.A.COTRUVO JR. JRNL TITL BIOCHEMICAL AND STRUCTURAL CHARACTERIZATION OF XOXG AND XOXJ JRNL TITL 2 AND THEIR ROLES IN LANTHANIDE-DEPENDENT METHANOL JRNL TITL 3 DEHYDROGENASE ACTIVITY. JRNL REF CHEMBIOCHEM V. 20 2360 2019 JRNL REFN ESSN 1439-7633 JRNL PMID 31017712 JRNL DOI 10.1002/CBIC.201900184 REMARK 2 REMARK 2 RESOLUTION. 2.27 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 : NULL REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.27 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 49.39 REMARK 3 MIN(FOBS/SIGMA_FOBS) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 93.7 REMARK 3 NUMBER OF REFLECTIONS : 11410 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.241 REMARK 3 R VALUE (WORKING SET) : 0.240 REMARK 3 FREE R VALUE : 0.279 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.810 REMARK 3 FREE R VALUE TEST SET COUNT : 549 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 49.4000 - 3.6000 1.00 2953 146 0.2071 0.2226 REMARK 3 2 3.6000 - 2.8500 1.00 2880 162 0.2566 0.3155 REMARK 3 3 2.8500 - 2.4900 1.00 2881 137 0.2780 0.3394 REMARK 3 4 2.4900 - 2.2700 0.75 2147 104 0.2817 0.3352 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) : 0.238 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 30.894 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 29.35 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 37.94 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 : 0.002 1699 REMARK 3 ANGLE : 0.532 2291 REMARK 3 CHIRALITY : 0.043 260 REMARK 3 PLANARITY : 0.004 289 REMARK 3 DIHEDRAL : 2.339 1038 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 6ONP COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 23-APR-19. REMARK 100 THE DEPOSITION ID IS D_1000240727. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 28-APR-17 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 8.5-9.0 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : ALS REMARK 200 BEAMLINE : 8.2.1 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.0 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 315R REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 12159 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.270 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 (%) : 93.7 REMARK 200 DATA REDUNDANCY : 5.400 REMARK 200 R MERGE (I) : 0.08800 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 19.6000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.27 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.30 REMARK 200 COMPLETENESS FOR SHELL (%) : NULL REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : 0.67400 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: SAD REMARK 200 SOFTWARE USED: CRANK2 REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 41.54 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.10 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.1 M TRIS PH 9.0, 18% PEG 6000, VAPOR REMARK 280 DIFFUSION, HANGING DROP, TEMPERATURE 298K 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 25.87950 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 1 REMARK 465 THR A 2 REMARK 465 ARG A 3 REMARK 465 SER A 4 REMARK 465 SER A 5 REMARK 465 ALA A 6 REMARK 465 PRO A 7 REMARK 465 VAL A 8 REMARK 465 SER A 9 REMARK 465 VAL A 10 REMARK 465 ALA A 11 REMARK 465 VAL A 12 REMARK 465 ALA A 13 REMARK 465 ALA A 14 REMARK 465 LEU A 15 REMARK 465 LEU A 16 REMARK 465 LEU A 17 REMARK 465 SER A 18 REMARK 465 ALA A 19 REMARK 465 GLY A 20 REMARK 465 ALA A 21 REMARK 465 ARG A 22 REMARK 465 PRO A 23 REMARK 465 ALA A 24 REMARK 465 HIS A 25 REMARK 465 ALA A 26 REMARK 465 GLN A 27 REMARK 465 HIS A 28 REMARK 465 LEU A 29 REMARK 465 PRO A 30 REMARK 465 ASP A 31 REMARK 465 LEU A 32 REMARK 465 VAL A 33 REMARK 465 THR A 34 REMARK 465 GLN A 35 REMARK 465 ASP A 36 REMARK 465 GLY A 81 REMARK 465 PRO A 82 REMARK 465 LEU A 89 REMARK 465 GLY A 90 REMARK 465 THR A 91 REMARK 465 GLY A 92 REMARK 465 LEU A 93 REMARK 465 SER A 101 REMARK 465 GLY A 102 REMARK 465 GLY A 103 REMARK 465 ASP A 104 REMARK 465 ILE A 105 REMARK 465 VAL A 106 REMARK 465 GLN A 107 REMARK 465 TYR A 170 REMARK 465 ALA A 171 REMARK 465 PHE A 172 REMARK 465 GLY A 173 REMARK 465 ALA A 174 REMARK 465 GLU A 175 REMARK 465 ARG A 176 REMARK 465 GLY A 225 REMARK 465 ARG A 226 REMARK 465 ARG A 238 REMARK 465 HIS A 239 REMARK 465 ASN A 240 REMARK 465 GLU A 274 REMARK 465 ASP A 275 REMARK 465 THR A 276 REMARK 465 LYS A 277 REMARK 465 PRO A 278 REMARK 465 LEU A 279 REMARK 465 ASP A 280 REMARK 465 ALA A 281 REMARK 465 ALA A 282 REMARK 465 ASP A 283 REMARK 465 GLU A 284 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 46 53.86 -149.00 REMARK 500 ARG A 255 34.75 -86.45 REMARK 500 REMARK 500 REMARK: NULL REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue EDO A 301 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue EDO A 302 DBREF 6ONP A 1 284 UNP C5B122 C5B122_METEA 1 284 SEQRES 1 A 284 MET THR ARG SER SER ALA PRO VAL SER VAL ALA VAL ALA SEQRES 2 A 284 ALA LEU LEU LEU SER ALA GLY ALA ARG PRO ALA HIS ALA SEQRES 3 A 284 GLN HIS LEU PRO ASP LEU VAL THR GLN ASP VAL LEU ARG SEQRES 4 A 284 VAL CYS SER ASP PRO GLY ASN MET PRO PHE SER GLU ARG SEQRES 5 A 284 LYS GLY GLY GLY PHE GLU ASN LYS ILE ALA GLN ILE VAL SEQRES 6 A 284 ALA ASP GLU LEU LYS VAL LYS LEU ARG TYR TYR TRP LEU SEQRES 7 A 284 THR GLN GLY PRO GLY PHE VAL ARG ASN THR LEU GLY THR SEQRES 8 A 284 GLY LEU CYS ASP LEU ILE ILE GLY THR SER GLY GLY ASP SEQRES 9 A 284 ILE VAL GLN ALA THR ASN PRO TYR TYR ARG SER ALA TYR SEQRES 10 A 284 VAL LEU VAL ALA ARG LYS GLY GLU LEU ALA ASP LEU LYS SEQRES 11 A 284 ARG LEU ASP ASP PRO ARG LEU LYS ASP ARG GLN ILE GLY SEQRES 12 A 284 ILE ILE ALA GLY THR PRO PRO SER ASN ARG LEU SER GLU SEQRES 13 A 284 LEU LYS LEU VAL GLY GLU ARG ILE HIS ALA TYR ALA PRO SEQRES 14 A 284 TYR ALA PHE GLY ALA GLU ARG LYS HIS GLN THR VAL ALA SEQRES 15 A 284 ALA GLU VAL ILE ALA ASP LEU ALA GLU LYS LYS ILE ASP SEQRES 16 A 284 VAL ALA ILE LEU TRP GLY PRO ALA ALA GLY TRP LEU ALA SEQRES 17 A 284 LYS GLN SER GLY VAL PRO MET ASP VAL VAL PRO LEU LEU SEQRES 18 A 284 HIS GLU PRO GLY ARG PRO PRO LEU THR PHE ARG VAL SER SEQRES 19 A 284 MET GLY VAL ARG HIS ASN GLU ASN ASP TRP LYS ARG SER SEQRES 20 A 284 LEU ASN THR VAL LEU ARG LYS ARG LYS ALA ASP ILE GLU SEQRES 21 A 284 ALA VAL LEU ARG GLU TYR GLU VAL PRO LEU LEU ALA GLU SEQRES 22 A 284 GLU ASP THR LYS PRO LEU ASP ALA ALA ASP GLU HET EDO A 301 4 HET EDO A 302 4 HETNAM EDO 1,2-ETHANEDIOL HETSYN EDO ETHYLENE GLYCOL FORMUL 2 EDO 2(C2 H6 O2) FORMUL 4 HOH *42(H2 O) HELIX 1 AA1 GLY A 56 LEU A 69 1 14 HELIX 2 AA2 PHE A 84 THR A 88 1 5 HELIX 3 AA3 ASP A 134 ARG A 140 5 7 HELIX 4 AA4 PRO A 149 LEU A 157 1 9 HELIX 5 AA5 THR A 180 GLU A 191 1 12 HELIX 6 AA6 GLY A 201 SER A 211 1 11 HELIX 7 AA7 ASN A 242 ARG A 255 1 14 HELIX 8 AA8 ARG A 255 TYR A 266 1 12 SHEET 1 AA1 2 LEU A 38 SER A 42 0 SHEET 2 AA1 2 LEU A 73 TRP A 77 1 O ARG A 74 N LEU A 38 SHEET 1 AA2 2 GLY A 45 ASN A 46 0 SHEET 2 AA2 2 SER A 50 GLU A 51 -1 O SER A 50 N ASN A 46 SHEET 1 AA3 6 ILE A 97 THR A 100 0 SHEET 2 AA3 6 THR A 230 GLY A 236 -1 O SER A 234 N THR A 100 SHEET 3 AA3 6 TYR A 113 ARG A 122 -1 N TYR A 113 O VAL A 233 SHEET 4 AA3 6 VAL A 196 TRP A 200 -1 O LEU A 199 N VAL A 118 SHEET 5 AA3 6 ILE A 142 ILE A 145 1 N GLY A 143 O VAL A 196 SHEET 6 AA3 6 ILE A 164 TYR A 167 1 O HIS A 165 N ILE A 142 SHEET 1 AA4 4 ILE A 97 THR A 100 0 SHEET 2 AA4 4 THR A 230 GLY A 236 -1 O SER A 234 N THR A 100 SHEET 3 AA4 4 TYR A 113 ARG A 122 -1 N TYR A 113 O VAL A 233 SHEET 4 AA4 4 MET A 215 PRO A 219 -1 O VAL A 218 N LEU A 119 SSBOND 1 CYS A 41 CYS A 94 1555 1555 2.03 CISPEP 1 MET A 47 PRO A 48 0 3.76 SITE 1 AC1 5 CYS A 41 SER A 42 GLU A 58 ILE A 98 SITE 2 AC1 5 GLY A 99 SITE 1 AC2 4 ALA A 183 ALA A 187 HOH A 404 HOH A 414 CRYST1 49.900 51.759 51.241 90.00 98.24 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 0.020040 0.000000 0.002901 0.00000 SCALE2 0.000000 0.019320 0.000000 0.00000 SCALE3 0.000000 0.000000 0.019719 0.00000