HEADER ISOMERASE 17-MAR-20 6YBR TITLE RT STRUCTURE OF GLUCOSE ISOMERASE OBTAINED AT 1.20 A RESOLUTION FROM TITLE 2 CRYSTAL GROWN IN A MYLAR 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 XYLOSE ISOMERASE, ISOMERASE EXPDTA X-RAY DIFFRACTION AUTHOR J.A.GAVIRA,S.MARTINEZ-RODRIGUEZ REVDAT 3 24-JAN-24 6YBR 1 REMARK REVDAT 2 19-AUG-20 6YBR 1 JRNL REVDAT 1 12-AUG-20 6YBR 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. 1.20 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) : 1.20 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 46.99 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.340 REMARK 3 COMPLETENESS FOR RANGE (%) : 100.0 REMARK 3 NUMBER OF REFLECTIONS : 149841 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.122 REMARK 3 R VALUE (WORKING SET) : 0.121 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 : 7490 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 46.9900 - 3.7300 1.00 5012 262 0.1273 0.1408 REMARK 3 2 3.7300 - 2.9600 1.00 4848 256 0.1209 0.1234 REMARK 3 3 2.9600 - 2.5900 1.00 4808 253 0.1298 0.1350 REMARK 3 4 2.5900 - 2.3500 1.00 4816 253 0.1242 0.1342 REMARK 3 5 2.3500 - 2.1800 1.00 4776 251 0.1107 0.1137 REMARK 3 6 2.1800 - 2.0500 1.00 4763 251 0.1087 0.1209 REMARK 3 7 2.0500 - 1.9500 1.00 4752 250 0.0997 0.1058 REMARK 3 8 1.9500 - 1.8600 1.00 4763 251 0.0963 0.1056 REMARK 3 9 1.8600 - 1.7900 1.00 4756 250 0.0966 0.1123 REMARK 3 10 1.7900 - 1.7300 1.00 4750 250 0.0917 0.1097 REMARK 3 11 1.7300 - 1.6800 1.00 4715 248 0.0895 0.0964 REMARK 3 12 1.6800 - 1.6300 1.00 4741 250 0.0827 0.1058 REMARK 3 13 1.6300 - 1.5900 1.00 4731 249 0.0887 0.1034 REMARK 3 14 1.5900 - 1.5500 1.00 4755 250 0.0943 0.1089 REMARK 3 15 1.5500 - 1.5100 1.00 4731 249 0.0953 0.1162 REMARK 3 16 1.5100 - 1.4800 1.00 4710 247 0.0964 0.1120 REMARK 3 17 1.4800 - 1.4500 1.00 4715 248 0.0970 0.1186 REMARK 3 18 1.4500 - 1.4200 1.00 4732 249 0.1005 0.1193 REMARK 3 19 1.4200 - 1.4000 1.00 4709 248 0.1053 0.1224 REMARK 3 20 1.4000 - 1.3700 1.00 4729 249 0.1141 0.1258 REMARK 3 21 1.3700 - 1.3500 1.00 4722 249 0.1360 0.1402 REMARK 3 22 1.3500 - 1.3300 1.00 4714 248 0.1590 0.1780 REMARK 3 23 1.3300 - 1.3100 1.00 4723 248 0.1868 0.1961 REMARK 3 24 1.3100 - 1.2900 1.00 4693 247 0.2376 0.2231 REMARK 3 25 1.2900 - 1.2800 1.00 4709 248 0.2828 0.3133 REMARK 3 26 1.2800 - 1.2600 1.00 4676 246 0.3128 0.3067 REMARK 3 27 1.2600 - 1.2400 1.00 4714 248 0.2602 0.2754 REMARK 3 28 1.2400 - 1.2300 1.00 4725 249 0.2708 0.2645 REMARK 3 29 1.2300 - 1.2100 1.00 4724 249 0.3165 0.3136 REMARK 3 30 1.2100 - 1.2000 0.99 4639 244 0.3564 0.3326 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) : 0.134 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 12.693 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 16.95 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 22.93 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 3517 REMARK 3 ANGLE : 0.889 4817 REMARK 3 CHIRALITY : 0.075 485 REMARK 3 PLANARITY : 0.007 680 REMARK 3 DIHEDRAL : 8.586 1951 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 6YBR COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 18-MAR-20. REMARK 100 THE DEPOSITION ID IS D_1292107362. 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 : 149874 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.200 REMARK 200 RESOLUTION RANGE LOW (A) : 46.990 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 100.0 REMARK 200 DATA REDUNDANCY : 8.860 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 17.0000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.20 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.24 REMARK 200 COMPLETENESS FOR SHELL (%) : NULL 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 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 46.99500 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 49.69000 REMARK 290 SMTRY3 5 0.000000 0.000000 1.000000 51.55000 REMARK 290 SMTRY1 6 -1.000000 0.000000 0.000000 46.99500 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 49.69000 REMARK 290 SMTRY3 6 0.000000 0.000000 1.000000 51.55000 REMARK 290 SMTRY1 7 -1.000000 0.000000 0.000000 46.99500 REMARK 290 SMTRY2 7 0.000000 1.000000 0.000000 49.69000 REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 51.55000 REMARK 290 SMTRY1 8 1.000000 0.000000 0.000000 46.99500 REMARK 290 SMTRY2 8 0.000000 -1.000000 0.000000 49.69000 REMARK 290 SMTRY3 8 0.000000 0.000000 -1.000000 51.55000 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 SOFTWARE DETERMINED QUATERNARY STRUCTURE: TETRAMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 32420 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 46110 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -280.0 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 -1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 350 BIOMT3 2 0.000000 0.000000 1.000000 0.00000 REMARK 350 BIOMT1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT2 3 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT3 3 0.000000 0.000000 -1.000000 206.20000 REMARK 350 BIOMT1 4 1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT2 4 0.000000 -1.000000 0.000000 0.00000 REMARK 350 BIOMT3 4 0.000000 0.000000 -1.000000 206.20000 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 513 LIES ON A SPECIAL POSITION. REMARK 375 HOH A 675 LIES ON A SPECIAL POSITION. REMARK 375 HOH A 749 LIES ON A SPECIAL POSITION. REMARK 375 HOH A 755 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 740 O HOH A 767 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 509 O HOH A 537 3557 2.10 REMARK 500 O HOH A 525 O HOH A 724 4557 2.14 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: COVALENT BOND ANGLES REMARK 500 REMARK 500 THE STEREOCHEMICAL PARAMETERS OF THE FOLLOWING RESIDUES REMARK 500 HAVE VALUES WHICH DEVIATE FROM EXPECTED VALUES BY MORE REMARK 500 THAN 6*RMSD (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 500 IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 STANDARD TABLE: REMARK 500 FORMAT: (10X,I3,1X,A3,1X,A1,I4,A1,3(1X,A4,2X),12X,F5.1) REMARK 500 REMARK 500 EXPECTED VALUES PROTEIN: ENGH AND HUBER, 1999 REMARK 500 EXPECTED VALUES NUCLEIC ACID: CLOWNEY ET AL 1996 REMARK 500 REMARK 500 M RES CSSEQI ATM1 ATM2 ATM3 REMARK 500 ARG A 266 NE - CZ - NH1 ANGL. DEV. = -3.8 DEGREES REMARK 500 ARG A 266 NE - CZ - NH2 ANGL. DEV. = 3.0 DEGREES 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 -73.32 -83.46 REMARK 500 GLU A 186 105.09 83.54 REMARK 500 GLU A 186 109.87 77.85 REMARK 500 ASN A 247 -168.01 -168.05 REMARK 500 LYS A 253 -171.10 -170.27 REMARK 500 ALA A 343 61.87 -150.79 REMARK 500 PHE A 357 -67.34 -154.86 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 526 O 101.3 95.9 REMARK 620 N 1 2 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 181 OE2 REMARK 620 2 GLU A 217 OE1 87.1 REMARK 620 3 ASP A 245 OD2 98.2 102.8 REMARK 620 4 ASP A 287 OD2 161.3 85.3 100.2 REMARK 620 5 HOH A 510 O 94.0 167.6 89.3 89.8 REMARK 620 6 HOH A 576 O 78.2 96.3 160.4 85.6 71.9 REMARK 620 N 1 2 3 4 5 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 217 OE2 REMARK 620 2 ASP A 255 OD1 107.6 REMARK 620 3 ASP A 255 OD2 162.4 57.0 REMARK 620 4 ASP A 257 OD1 90.4 82.4 95.4 REMARK 620 5 HOH A 653 O 104.1 147.4 92.6 89.9 REMARK 620 N 1 2 3 4 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 NA A 404 NA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 GLN A 222 OE1 REMARK 620 2 GLN A 249 O 74.2 REMARK 620 3 HOH A 645 O 104.1 160.7 REMARK 620 N 1 2 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 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue NA A 404 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 6YBO RELATED DB: PDB REMARK 900 SAME PROTEIN & CITATION REMARK 900 RELATED ID: 6YBF RELATED DB: PDB REMARK 900 ENTRIES FOR THE SAME CITATION REMARK 900 RELATED ID: 6YBI RELATED DB: PDB REMARK 900 ENTRIES FOR THE SAME CITATION DBREF 6YBR 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 HET NA A 404 1 HETNAM MG MAGNESIUM ION HETNAM NA SODIUM ION FORMUL 2 MG 2(MG 2+) FORMUL 4 NA 2(NA 1+) FORMUL 6 HOH *291(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 MET A 88 THR A 90 1 N ALA A 89 O VAL A 135 SHEET 5 AA1 8 GLY A 50 HIS A 54 1 N PHE A 53 O THR A 90 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 OE2 GLU A 181 MG MG A 402 1555 1555 2.05 LINK OH TYR A 212 NA NA A 403 1555 1555 2.91 LINK OE2 GLU A 217 MG MG A 401 1555 1555 2.05 LINK OE1 GLU A 217 MG MG A 402 1555 1555 2.14 LINK OE1 GLN A 222 NA NA A 404 1555 1555 2.72 LINK OD2 ASP A 245 MG MG A 402 1555 1555 2.04 LINK O GLN A 249 NA NA A 404 1555 1555 3.12 LINK OD1 ASP A 255 MG MG A 401 1555 1555 2.34 LINK OD2 ASP A 255 MG MG A 401 1555 1555 2.25 LINK OD1 ASP A 257 MG MG A 401 1555 1555 2.21 LINK OD2 ASP A 287 MG MG A 402 1555 1555 2.09 LINK MG MG A 401 O HOH A 653 1555 1555 2.19 LINK MG MG A 402 O HOH A 510 1555 1555 2.40 LINK MG MG A 402 O HOH A 576 1555 1555 2.28 LINK NA NA A 403 O HOH A 526 1555 1555 2.83 LINK NA NA A 404 O HOH A 645 1555 1555 2.88 CISPEP 1 GLU A 186 PRO A 187 0 17.84 CISPEP 2 GLU A 186 PRO A 187 0 11.29 SITE 1 AC1 5 GLU A 217 HIS A 220 ASP A 255 ASP A 257 SITE 2 AC1 5 HOH A 653 SITE 1 AC2 6 GLU A 181 GLU A 217 ASP A 245 ASP A 287 SITE 2 AC2 6 HOH A 510 HOH A 576 SITE 1 AC3 5 ASP A 163 GLU A 207 ARG A 208 TYR A 212 SITE 2 AC3 5 HOH A 526 SITE 1 AC4 7 GLN A 222 GLY A 248 GLN A 249 ALA A 262 SITE 2 AC4 7 GLY A 263 ASP A 264 HOH A 645 CRYST1 93.990 99.380 103.100 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 0.010639 0.000000 0.000000 0.00000 SCALE2 0.000000 0.010062 0.000000 0.00000 SCALE3 0.000000 0.000000 0.009699 0.00000