PDB Short entry for 6YBO HEADER ISOMERASE 17-MAR-20 6YBO TITLE RT STRUCTURE OF GLUCOSE ISOMERASE OBTAINED AT 1.06 A RESOLUTION FROM TITLE 2 CRYSTAL GROWN IN A KAPTON MICROCHIP. COMPND MOL_ID: 1; COMPND 2 MOLECULE: XYLOSE ISOMERASE; COMPND 3 CHAIN: A; COMPND 4 EC: 5.3.1.5 SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: STREPTOMYCES RUBIGINOSUS; SOURCE 3 ORGANISM_TAXID: 1929 KEYWDS D-XYLOSE KETOL ISOMERASE, ISOMERASE EXPDTA X-RAY DIFFRACTION AUTHOR J.A.GAVIRA,S.MARTINEZ-RODRIGUEZ REVDAT 3 24-JAN-24 6YBO 1 REMARK REVDAT 2 19-AUG-20 6YBO 1 JRNL REVDAT 1 12-AUG-20 6YBO 0 JRNL AUTH J.A.GAVIRA,I.RODRIGUEZ-RUIZ,S.MARTINEZ-RODRIGUEZ,S.BASU, JRNL AUTH 2 S.TEYCHENE,A.A.MCCARTHY,C.MUELLER-DIECKMAN JRNL TITL ATTAINING ATOMIC RESOLUTION FROM IN SITU DATA COLLECTION AT JRNL TITL 2 ROOM TEMPERATURE USING COUNTER-DIFFUSION-BASED LOW-COST JRNL TITL 3 MICROCHIPS. JRNL REF ACTA CRYSTALLOGR D STRUCT V. 76 751 2020 JRNL REF 2 BIOL JRNL REFN ISSN 2059-7983 JRNL PMID 32744257 JRNL DOI 10.1107/S2059798320008475 REMARK 2 REMARK 2 RESOLUTION. 1.06 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.15.2_3472 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) : 1.06 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 41.12 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.340 REMARK 3 COMPLETENESS FOR RANGE (%) : 92.3 REMARK 3 NUMBER OF REFLECTIONS : 199958 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.123 REMARK 3 R VALUE (WORKING SET) : 0.123 REMARK 3 FREE R VALUE : 0.131 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.000 REMARK 3 FREE R VALUE TEST SET COUNT : 9998 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 41.1200 - 3.2900 1.00 7185 379 0.1288 0.1354 REMARK 3 2 3.2900 - 2.6100 1.00 7007 369 0.1292 0.1353 REMARK 3 3 2.6100 - 2.2800 1.00 6948 365 0.1216 0.1297 REMARK 3 4 2.2800 - 2.0700 1.00 6912 364 0.1054 0.1121 REMARK 3 5 2.0700 - 1.9300 1.00 6919 364 0.1003 0.1048 REMARK 3 6 1.9300 - 1.8100 1.00 6875 362 0.0995 0.1106 REMARK 3 7 1.8100 - 1.7200 1.00 6868 362 0.0978 0.1048 REMARK 3 8 1.7200 - 1.6500 1.00 6847 360 0.0925 0.1052 REMARK 3 9 1.6500 - 1.5800 1.00 6858 361 0.0852 0.0929 REMARK 3 10 1.5800 - 1.5300 1.00 6864 361 0.0828 0.0916 REMARK 3 11 1.5300 - 1.4800 1.00 6860 361 0.0830 0.0865 REMARK 3 12 1.4800 - 1.4400 1.00 6857 361 0.0869 0.1009 REMARK 3 13 1.4400 - 1.4000 1.00 6828 359 0.0950 0.1276 REMARK 3 14 1.4000 - 1.3700 1.00 6851 361 0.1038 0.1133 REMARK 3 15 1.3700 - 1.3400 1.00 6818 359 0.1089 0.1218 REMARK 3 16 1.3400 - 1.3100 1.00 6849 360 0.1112 0.1184 REMARK 3 17 1.3100 - 1.2800 1.00 6814 359 0.1254 0.1340 REMARK 3 18 1.2800 - 1.2600 1.00 6778 357 0.1323 0.1427 REMARK 3 19 1.2600 - 1.2300 1.00 6848 360 0.1425 0.1552 REMARK 3 20 1.2300 - 1.2100 1.00 6833 360 0.1568 0.1554 REMARK 3 21 1.2100 - 1.1900 1.00 6782 357 0.1668 0.1750 REMARK 3 22 1.1900 - 1.1800 1.00 6796 357 0.1748 0.1856 REMARK 3 23 1.1800 - 1.1600 0.99 6745 354 0.1918 0.1882 REMARK 3 24 1.1600 - 1.1400 0.97 6645 350 0.2182 0.2257 REMARK 3 25 1.1400 - 1.1300 0.90 6137 323 0.2559 0.2717 REMARK 3 26 1.1300 - 1.1100 0.85 5775 303 0.3203 0.3500 REMARK 3 27 1.1100 - 1.1000 0.77 5231 276 0.3338 0.3483 REMARK 3 28 1.1000 - 1.0800 0.46 3160 166 0.3493 0.3193 REMARK 3 29 1.0800 - 1.0700 0.40 2730 145 0.3793 0.4283 REMARK 3 30 1.0700 - 1.0600 0.34 2340 123 0.3693 0.4002 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) : 0.091 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 13.003 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 13.05 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 20.18 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 : 0.005 3567 REMARK 3 ANGLE : 0.904 4900 REMARK 3 CHIRALITY : 0.075 494 REMARK 3 PLANARITY : 0.007 690 REMARK 3 DIHEDRAL : 7.561 2532 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 6YBO COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 17-MAR-20. REMARK 100 THE DEPOSITION ID IS D_1292107353. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 06-MAR-17 REMARK 200 TEMPERATURE (KELVIN) : 293.5 REMARK 200 PH : 7.0 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : ESRF REMARK 200 BEAMLINE : ID30B REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.9763 REMARK 200 MONOCHROMATOR : SI(111) REMARK 200 OPTICS : BE CRL LENSES FOR VERTICAL REMARK 200 FOCUSING AND RH/PT/SI COATED REMARK 200 ELLIPITCAL MIRROR FOR HORIZONTAL REMARK 200 FOCUSING REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS PILATUS3 6M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : AIMLESS REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 200000 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.060 REMARK 200 RESOLUTION RANGE LOW (A) : 41.120 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 92.3 REMARK 200 DATA REDUNDANCY : 7.930 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 8.4000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.06 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.09 REMARK 200 COMPLETENESS FOR SHELL (%) : 40.2 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 <I/SIGMA(I)> 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: 4A8I REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 54.00 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.70 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.1 M MGCL2, 10% W/V PEG 1K, 0.1 M REMARK 280 HEPES PH 7.0, COUNTER-DIFFUSION, TEMPERATURE 293.5K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: I 2 2 2 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,-Z REMARK 290 4555 X,-Y,-Z REMARK 290 5555 X+1/2,Y+1/2,Z+1/2 REMARK 290 6555 -X+1/2,-Y+1/2,Z+1/2 REMARK 290 7555 -X+1/2,Y+1/2,-Z+1/2 REMARK 290 8555 X+1/2,-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 0.00000 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 4 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 5 1.000000 0.000000 0.000000 46.97000 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 49.68500 REMARK 290 SMTRY3 5 0.000000 0.000000 1.000000 51.52000 REMARK 290 SMTRY1 6 -1.000000 0.000000 0.000000 46.97000 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 49.68500 REMARK 290 SMTRY3 6 0.000000 0.000000 1.000000 51.52000 REMARK 290 SMTRY1 7 -1.000000 0.000000 0.000000 46.97000 REMARK 290 SMTRY2 7 0.000000 1.000000 0.000000 49.68500 REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 51.52000 REMARK 290 SMTRY1 8 1.000000 0.000000 0.000000 46.97000 REMARK 290 SMTRY2 8 0.000000 -1.000000 0.000000 49.68500 REMARK 290 SMTRY3 8 0.000000 0.000000 -1.000000 51.52000 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 375 REMARK 375 SPECIAL POSITION REMARK 375 THE FOLLOWING ATOMS ARE FOUND TO BE WITHIN 0.15 ANGSTROMS REMARK 375 OF A SYMMETRY RELATED ATOM AND ARE ASSUMED TO BE ON SPECIAL REMARK 375 POSITIONS. REMARK 375 REMARK 375 ATOM RES CSSEQI REMARK 375 HOH A 746 LIES ON A SPECIAL POSITION. 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 ASN A 2 REMARK 465 GLY A 388 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 573 O HOH A 727 1.96 REMARK 500 O HOH A 556 O HOH A 734 2.01 REMARK 500 OD1 ASP A 297 O HOH A 501 2.09 REMARK 500 O HOH A 524 O HOH A 770 2.10 REMARK 500 O HOH A 506 O HOH A 754 2.12 REMARK 500 O HOH A 529 O HOH A 683 2.12 REMARK 500 O HOH A 527 O HOH A 770 2.13 REMARK 500 O HOH A 728 O HOH A 760 2.16 REMARK 500 O HOH A 734 O HOH A 736 2.17 REMARK 500 OE2 GLU A 337 O HOH A 502 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 O HOH A 504 O HOH A 525 3557 2.07 REMARK 500 O HOH A 735 O HOH A 750 4557 2.11 REMARK 500 O HOH A 517 O HOH A 761 4557 2.13 REMARK 500 O HOH A 674 O HOH A 691 2555 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 THR A 17 -72.90 -83.77 REMARK 500 GLU A 186 104.31 83.88 REMARK 500 GLU A 186 113.65 75.69 REMARK 500 ASN A 247 -167.70 -168.67 REMARK 500 LYS A 253 -171.25 -170.19 REMARK 500 ALA A 343 60.50 -151.13 REMARK 500 PHE A 357 -69.36 -154.63 REMARK 500 REMARK 500 REMARK: NULL REMARK 620 REMARK 620 METAL COORDINATION REMARK 620 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 620 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE): REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 NA A 403 NA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP A 163 OD1 REMARK 620 2 TYR A 212 OH 110.0 REMARK 620 3 HOH A 534 O 101.9 95.0 REMARK 620 N 1 2 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MG A 401 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 GLU A 181 OE2 REMARK 620 2 GLU A 181 OE2 16.3 REMARK 620 3 GLU A 217 OE1 91.3 88.9 REMARK 620 4 ASP A 245 OD2 102.9 88.1 106.2 REMARK 620 5 ASP A 287 OD2 155.7 170.5 86.0 101.0 REMARK 620 6 HOH A 509 O 89.0 95.5 164.8 88.5 87.5 REMARK 620 7 HOH A 513 O 71.5 87.8 96.2 157.2 84.8 69.6 REMARK 620 N 1 2 3 4 5 6 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MG A 402 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 GLU A 217 OE2 REMARK 620 2 ASP A 255 OD1 107.1 REMARK 620 3 ASP A 255 OD2 162.5 57.4 REMARK 620 4 ASP A 257 OD1 89.9 82.7 95.4 REMARK 620 5 HOH A 627 O 104.7 147.3 92.0 89.8 REMARK 620 N 1 2 3 4 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue MG A 401 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue MG A 402 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue NA A 403 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 6YBF RELATED DB: PDB REMARK 900 PDB ENTRIES FOR THE SAME CITATION REMARK 900 RELATED ID: 6YBI RELATED DB: PDB REMARK 900 PDB ENTRIES FOR THE SAME CITATION DBREF 6YBO A 1 388 UNP P24300 XYLA_STRRU 1 388 SEQRES 1 A 388 MET ASN TYR GLN PRO THR PRO GLU ASP ARG PHE THR PHE SEQRES 2 A 388 GLY LEU TRP THR VAL GLY TRP GLN GLY ARG ASP PRO PHE SEQRES 3 A 388 GLY ASP ALA THR ARG ARG ALA LEU ASP PRO VAL GLU SER SEQRES 4 A 388 VAL ARG ARG LEU ALA GLU LEU GLY ALA HIS GLY VAL THR SEQRES 5 A 388 PHE HIS ASP ASP ASP LEU ILE PRO PHE GLY SER SER ASP SEQRES 6 A 388 SER GLU ARG GLU GLU HIS VAL LYS ARG PHE ARG GLN ALA SEQRES 7 A 388 LEU ASP ASP THR GLY MET LYS VAL PRO MET ALA THR THR SEQRES 8 A 388 ASN LEU PHE THR HIS PRO VAL PHE LYS ASP GLY GLY PHE SEQRES 9 A 388 THR ALA ASN ASP ARG ASP VAL ARG ARG TYR ALA LEU ARG SEQRES 10 A 388 LYS THR ILE ARG ASN ILE ASP LEU ALA VAL GLU LEU GLY SEQRES 11 A 388 ALA GLU THR TYR VAL ALA TRP GLY GLY ARG GLU GLY ALA SEQRES 12 A 388 GLU SER GLY GLY ALA LYS ASP VAL ARG ASP ALA LEU ASP SEQRES 13 A 388 ARG MET LYS GLU ALA PHE ASP LEU LEU GLY GLU TYR VAL SEQRES 14 A 388 THR SER GLN GLY TYR ASP ILE ARG PHE ALA ILE GLU PRO SEQRES 15 A 388 LYS PRO ASN GLU PRO ARG GLY ASP ILE LEU LEU PRO THR SEQRES 16 A 388 VAL GLY HIS ALA LEU ALA PHE ILE GLU ARG LEU GLU ARG SEQRES 17 A 388 PRO GLU LEU TYR GLY VAL ASN PRO GLU VAL GLY HIS GLU SEQRES 18 A 388 GLN MET ALA GLY LEU ASN PHE PRO HIS GLY ILE ALA GLN SEQRES 19 A 388 ALA LEU TRP ALA GLY LYS LEU PHE HIS ILE ASP LEU ASN SEQRES 20 A 388 GLY GLN ASN GLY ILE LYS TYR ASP GLN ASP LEU ARG PHE SEQRES 21 A 388 GLY ALA GLY ASP LEU ARG ALA ALA PHE TRP LEU VAL ASP SEQRES 22 A 388 LEU LEU GLU SER ALA GLY TYR SER GLY PRO ARG HIS PHE SEQRES 23 A 388 ASP PHE LYS PRO PRO ARG THR GLU ASP PHE ASP GLY VAL SEQRES 24 A 388 TRP ALA SER ALA ALA GLY CYS MET ARG ASN TYR LEU ILE SEQRES 25 A 388 LEU LYS GLU ARG ALA ALA ALA PHE ARG ALA ASP PRO GLU SEQRES 26 A 388 VAL GLN GLU ALA LEU ARG ALA SER ARG LEU ASP GLU LEU SEQRES 27 A 388 ALA ARG PRO THR ALA ALA ASP GLY LEU GLN ALA LEU LEU SEQRES 28 A 388 ASP ASP ARG SER ALA PHE GLU GLU PHE ASP VAL ASP ALA SEQRES 29 A 388 ALA ALA ALA ARG GLY MET ALA PHE GLU ARG LEU ASP GLN SEQRES 30 A 388 LEU ALA MET ASP HIS LEU LEU GLY ALA ARG GLY HET MG A 401 1 HET MG A 402 1 HET NA A 403 1 HETNAM MG MAGNESIUM ION HETNAM NA SODIUM ION FORMUL 2 MG 2(MG 2+) FORMUL 4 NA NA 1+ FORMUL 5 HOH *281(H2 O) HELIX 1 AA1 THR A 6 ASP A 9 5 4 HELIX 2 AA2 LEU A 15 GLY A 19 1 5 HELIX 3 AA3 ASP A 35 GLY A 47 1 13 HELIX 4 AA4 ASP A 55 ILE A 59 1 5 HELIX 5 AA5 SER A 64 GLY A 83 1 20 HELIX 6 AA6 HIS A 96 LYS A 100 5 5 HELIX 7 AA7 ASP A 108 LEU A 129 1 22 HELIX 8 AA8 SER A 145 LYS A 149 5 5 HELIX 9 AA9 ASP A 150 GLY A 173 1 24 HELIX 10 AB1 THR A 195 GLU A 204 1 10 HELIX 11 AB2 ARG A 208 GLU A 210 5 3 HELIX 12 AB3 GLU A 217 MET A 223 1 7 HELIX 13 AB4 ASN A 227 ALA A 238 1 12 HELIX 14 AB5 ASP A 264 GLY A 279 1 16 HELIX 15 AB6 ASP A 295 ASP A 323 1 29 HELIX 16 AB7 ASP A 323 SER A 333 1 11 HELIX 17 AB8 ARG A 334 ALA A 339 1 6 HELIX 18 AB9 GLY A 346 ASP A 353 1 8 HELIX 19 AC1 ARG A 354 PHE A 357 5 4 HELIX 20 AC2 ASP A 361 ARG A 368 1 8 HELIX 21 AC3 ALA A 371 GLY A 385 1 15 SHEET 1 AA1 8 TYR A 212 VAL A 214 0 SHEET 2 AA1 8 ARG A 177 ILE A 180 1 N ILE A 180 O GLY A 213 SHEET 3 AA1 8 THR A 133 ALA A 136 1 N TYR A 134 O ARG A 177 SHEET 4 AA1 8 LYS A 85 THR A 90 1 N ALA A 89 O VAL A 135 SHEET 5 AA1 8 GLY A 50 HIS A 54 1 N VAL A 51 O LYS A 85 SHEET 6 AA1 8 PHE A 11 GLY A 14 1 N PHE A 13 O THR A 52 SHEET 7 AA1 8 ARG A 284 PHE A 286 1 O PHE A 286 N THR A 12 SHEET 8 AA1 8 ASP A 245 LEU A 246 1 N LEU A 246 O HIS A 285 SHEET 1 AA2 2 GLY A 142 ALA A 143 0 SHEET 2 AA2 2 ASP A 190 ILE A 191 -1 O ASP A 190 N ALA A 143 LINK OD1 ASP A 163 NA NA A 403 1555 1555 2.73 LINK OE2AGLU A 181 MG MG A 401 1555 1555 1.98 LINK OE2BGLU A 181 MG MG A 401 1555 1555 2.00 LINK OH TYR A 212 NA NA A 403 1555 1555 2.89 LINK OE1 GLU A 217 MG MG A 401 1555 1555 2.10 LINK OE2 GLU A 217 MG MG A 402 1555 1555 2.04 LINK OD2 ASP A 245 MG MG A 401 1555 1555 2.07 LINK OD1 ASP A 255 MG MG A 402 1555 1555 2.32 LINK OD2 ASP A 255 MG MG A 402 1555 1555 2.22 LINK OD1 ASP A 257 MG MG A 402 1555 1555 2.18 LINK OD2 ASP A 287 MG MG A 401 1555 1555 2.12 LINK MG MG A 401 O HOH A 509 1555 1555 2.30 LINK MG MG A 401 O HOH A 513 1555 1555 2.28 LINK MG MG A 402 O HOH A 627 1555 1555 2.17 LINK NA NA A 403 O HOH A 534 1555 1555 2.82 CISPEP 1 GLU A 186 PRO A 187 0 19.64 CISPEP 2 GLU A 186 PRO A 187 0 7.82 SITE 1 AC1 6 GLU A 181 GLU A 217 ASP A 245 ASP A 287 SITE 2 AC1 6 HOH A 509 HOH A 513 SITE 1 AC2 5 GLU A 217 HIS A 220 ASP A 255 ASP A 257 SITE 2 AC2 5 HOH A 627 SITE 1 AC3 5 ASP A 163 GLU A 207 ARG A 208 TYR A 212 SITE 2 AC3 5 HOH A 534 CRYST1 93.940 99.370 103.040 90.00 90.00 90.00 I 2 2 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 0.010645 0.000000 0.000000 0.00000 SCALE2 0.000000 0.010063 0.000000 0.00000 SCALE3 0.000000 0.000000 0.009705 0.00000