HEADER ISOMERASE 28-AUG-18 6HHN TITLE CRYSTAL STRUCTURE OF L-RHAMNOSE MUTAROTASE FA22100 FROM FORMOSA TITLE 2 AGARIPHILA COMPND MOL_ID: 1; COMPND 2 MOLECULE: L-RHAMNOSE MUTAROTASE; COMPND 3 CHAIN: A; COMPND 4 EC: 5.1.3.32; COMPND 5 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: FORMOSA AGARIPHILA; SOURCE 3 ORGANISM_TAXID: 320324; SOURCE 4 GENE: BN863_22100; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 6 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS MONOSACCHARIDE MUTAROTASE RHAMNOSE FORMOSA AGARIPHILA, ISOMERASE EXPDTA X-RAY DIFFRACTION AUTHOR T.RORET,A.PRECHOUX,G.MICHEL,M.CZJZEK REVDAT 4 17-JAN-24 6HHN 1 REMARK REVDAT 3 31-JUL-19 6HHN 1 JRNL REVDAT 2 24-JUL-19 6HHN 1 JRNL REVDAT 1 26-JUN-19 6HHN 0 JRNL AUTH L.REISKY,A.PRECHOUX,M.K.ZUHLKE,M.BAUMGEN,C.S.ROBB,N.GERLACH, JRNL AUTH 2 T.RORET,C.STANETTY,R.LAROCQUE,G.MICHEL,T.SONG,S.MARKERT, JRNL AUTH 3 F.UNFRIED,M.D.MIHOVILOVIC,A.TRAUTWEIN-SCHULT,D.BECHER, JRNL AUTH 4 T.SCHWEDER,U.T.BORNSCHEUER,J.H.HEHEMANN JRNL TITL A MARINE BACTERIAL ENZYMATIC CASCADE DEGRADES THE ALGAL JRNL TITL 2 POLYSACCHARIDE ULVAN. JRNL REF NAT.CHEM.BIOL. V. 15 803 2019 JRNL REFN ESSN 1552-4469 JRNL PMID 31285597 JRNL DOI 10.1038/S41589-019-0311-9 REMARK 2 REMARK 2 RESOLUTION. 1.47 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 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) : 1.47 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 43.17 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.360 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.3 REMARK 3 NUMBER OF REFLECTIONS : 24172 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.149 REMARK 3 R VALUE (WORKING SET) : 0.148 REMARK 3 FREE R VALUE : 0.172 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.890 REMARK 3 FREE R VALUE TEST SET COUNT : 1183 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 43.1846 - 2.9329 0.99 3069 156 0.1626 0.1818 REMARK 3 2 2.9329 - 2.3280 1.00 2930 148 0.1593 0.1583 REMARK 3 3 2.3280 - 2.0337 1.00 2887 150 0.1300 0.1703 REMARK 3 4 2.0337 - 1.8478 1.00 2875 152 0.1256 0.1606 REMARK 3 5 1.8478 - 1.7153 1.00 2858 143 0.1247 0.1449 REMARK 3 6 1.7153 - 1.6142 1.00 2817 151 0.1177 0.1882 REMARK 3 7 1.6142 - 1.5333 0.99 2827 139 0.1171 0.1863 REMARK 3 8 1.5333 - 1.4666 0.97 2726 144 0.1475 0.2169 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) : 0.120 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 18.250 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 : 0.008 874 REMARK 3 ANGLE : 0.889 1180 REMARK 3 CHIRALITY : 0.083 121 REMARK 3 PLANARITY : 0.005 154 REMARK 3 DIHEDRAL : 22.347 334 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 6HHN COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 28-AUG-18. REMARK 100 THE DEPOSITION ID IS D_1200011688. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 05-JUN-18 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 : SOLEIL REMARK 200 BEAMLINE : PROXIMA 1 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.979140 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS PILATUS 6M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : AIMLESS REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 24225 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.470 REMARK 200 RESOLUTION RANGE LOW (A) : 43.170 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.5 REMARK 200 DATA REDUNDANCY : 9.100 REMARK 200 R MERGE (I) : 0.03200 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 32.3000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.47 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.55 REMARK 200 COMPLETENESS FOR SHELL (%) : 97.2 REMARK 200 DATA REDUNDANCY IN SHELL : 8.50 REMARK 200 R MERGE FOR SHELL (I) : 0.29500 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 6.600 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: 2QLX REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 51.74 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.55 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 100 MM SODIUM ACETATE PH4.6 4.3 M REMARK 280 SODIUM FORMATE, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 293K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 43 21 2 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,-Y,Z+1/2 REMARK 290 3555 -Y+1/2,X+1/2,Z+3/4 REMARK 290 4555 Y+1/2,-X+1/2,Z+1/4 REMARK 290 5555 -X+1/2,Y+1/2,-Z+3/4 REMARK 290 6555 X+1/2,-Y+1/2,-Z+1/4 REMARK 290 7555 Y,X,-Z REMARK 290 8555 -Y,-X,-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 27.20350 REMARK 290 SMTRY1 3 0.000000 -1.000000 0.000000 35.45650 REMARK 290 SMTRY2 3 1.000000 0.000000 0.000000 35.45650 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 40.80525 REMARK 290 SMTRY1 4 0.000000 1.000000 0.000000 35.45650 REMARK 290 SMTRY2 4 -1.000000 0.000000 0.000000 35.45650 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 13.60175 REMARK 290 SMTRY1 5 -1.000000 0.000000 0.000000 35.45650 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 35.45650 REMARK 290 SMTRY3 5 0.000000 0.000000 -1.000000 40.80525 REMARK 290 SMTRY1 6 1.000000 0.000000 0.000000 35.45650 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 35.45650 REMARK 290 SMTRY3 6 0.000000 0.000000 -1.000000 13.60175 REMARK 290 SMTRY1 7 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY2 7 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 8 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY2 8 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 8 0.000000 0.000000 -1.000000 27.20350 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: DIMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 3190 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 10720 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -23.0 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 350 BIOMT1 2 0.000000 -1.000000 0.000000 0.00000 REMARK 350 BIOMT2 2 -1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT3 2 0.000000 0.000000 -1.000000 -27.20350 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 -10 REMARK 465 GLY A -9 REMARK 465 SER A -8 REMARK 465 SER A -7 REMARK 465 HIS A -6 REMARK 465 HIS A -5 REMARK 465 HIS A -4 REMARK 465 HIS A -3 REMARK 465 HIS A -2 REMARK 465 HIS A -1 REMARK 465 GLY A 0 REMARK 465 HIS A 61 REMARK 465 GLY A 62 REMARK 465 GLY A 63 REMARK 465 SER A 64 REMARK 465 GLN A 65 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 O HOH A 271 O HOH A 276 1.92 REMARK 500 O HOH A 203 O HOH A 238 1.95 REMARK 500 O HOH A 297 O HOH A 298 2.05 REMARK 500 O HOH A 263 O HOH A 307 2.10 REMARK 500 O HOH A 204 O HOH A 280 2.18 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 O HOH A 302 O HOH A 309 4445 1.81 REMARK 500 O HOH A 308 O HOH A 322 3454 1.89 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 ASN A 90 -0.53 77.38 REMARK 500 REMARK 500 REMARK: NULL DBREF 6HHN A 2 104 UNP T2KM13 T2KM13_9FLAO 2 104 SEQADV 6HHN MET A -10 UNP T2KM13 INITIATING METHIONINE SEQADV 6HHN GLY A -9 UNP T2KM13 EXPRESSION TAG SEQADV 6HHN SER A -8 UNP T2KM13 EXPRESSION TAG SEQADV 6HHN SER A -7 UNP T2KM13 EXPRESSION TAG SEQADV 6HHN HIS A -6 UNP T2KM13 EXPRESSION TAG SEQADV 6HHN HIS A -5 UNP T2KM13 EXPRESSION TAG SEQADV 6HHN HIS A -4 UNP T2KM13 EXPRESSION TAG SEQADV 6HHN HIS A -3 UNP T2KM13 EXPRESSION TAG SEQADV 6HHN HIS A -2 UNP T2KM13 EXPRESSION TAG SEQADV 6HHN HIS A -1 UNP T2KM13 EXPRESSION TAG SEQADV 6HHN GLY A 0 UNP T2KM13 EXPRESSION TAG SEQADV 6HHN SER A 1 UNP T2KM13 EXPRESSION TAG SEQRES 1 A 115 MET GLY SER SER HIS HIS HIS HIS HIS HIS GLY SER GLU SEQRES 2 A 115 ARG LEU ALA PHE LYS MET LYS LEU ASN LYS GLY GLN LYS SEQRES 3 A 115 GLN ALA TYR LYS GLU ARG HIS ASP GLN LEU TRP PRO GLU SEQRES 4 A 115 LEU LYS GLN LEU LEU LYS ASP ASN GLY VAL SER GLU TYR SEQRES 5 A 115 SER ILE PHE ILE ASP GLU GLU THR ASN THR LEU PHE ALA SEQRES 6 A 115 PHE GLN LYS VAL SER GLY HIS GLY GLY SER GLN ASP LEU SEQRES 7 A 115 ALA ASN ASN GLU ILE VAL LYS LYS TRP TRP ASP PHE MET SEQRES 8 A 115 ALA ASP ILE MET GLN VAL ASN PRO ASP ASN SER PRO VAL SEQRES 9 A 115 SER ILE PRO LEU GLU GLU VAL PHE TYR MET GLU FORMUL 2 HOH *123(H2 O) HELIX 1 AA1 GLN A 14 GLN A 24 1 11 HELIX 2 AA2 TRP A 26 ASN A 36 1 11 HELIX 3 AA3 GLU A 47 THR A 49 5 3 HELIX 4 AA4 ASP A 66 ASN A 69 5 4 HELIX 5 AA5 ASN A 70 ALA A 81 1 12 SHEET 1 AA1 4 VAL A 38 ASP A 46 0 SHEET 2 AA1 4 THR A 51 VAL A 58 -1 O PHE A 53 N PHE A 44 SHEET 3 AA1 4 GLU A 2 LYS A 9 -1 N PHE A 6 O ALA A 54 SHEET 4 AA1 4 ILE A 95 LEU A 97 -1 O ILE A 95 N LYS A 7 CRYST1 70.913 70.913 54.407 90.00 90.00 90.00 P 43 21 2 8 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 0.014102 0.000000 0.000000 0.00000 SCALE2 0.000000 0.014102 0.000000 0.00000 SCALE3 0.000000 0.000000 0.018380 0.00000