HEADER ISOMERASE 14-APR-15 4ZB5 TITLE A FORM OF GLUCOSE ISOMERASE COLLECTED AT 100K. COMPND MOL_ID: 1; COMPND 2 MOLECULE: XYLOSE ISOMERASE; COMPND 3 CHAIN: A; COMPND 4 EC: 5.3.1.5; COMPND 5 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: STREPTOMYCES RUBIGINOSUS; SOURCE 3 ORGANISM_TAXID: 1929; SOURCE 4 GENE: XYLA; SOURCE 5 EXPRESSION_SYSTEM: STREPTOMYCES RUBIGINOSUS; SOURCE 6 EXPRESSION_SYSTEM_TAXID: 1929 KEYWDS ISOMERASE EXPDTA X-RAY DIFFRACTION AUTHOR J.SANDY REVDAT 4 10-JAN-24 4ZB5 1 HETSYN REVDAT 3 29-JUL-20 4ZB5 1 COMPND REMARK HETNAM SITE REVDAT 3 2 1 ATOM REVDAT 2 11-MAY-16 4ZB5 1 JRNL REVDAT 1 23-MAR-16 4ZB5 0 JRNL AUTH C.M.LOBLEY,J.SANDY,J.SANCHEZ-WEATHERBY,M.MAZZORANA,T.KROJER, JRNL AUTH 2 R.P.NOWAK,T.L.SORENSEN JRNL TITL A GENERIC PROTOCOL FOR PROTEIN CRYSTAL DEHYDRATION USING THE JRNL TITL 2 HC1B HUMIDITY CONTROLLER. JRNL REF ACTA CRYSTALLOGR D STRUCT V. 72 629 2016 JRNL REF 2 BIOL JRNL REFN ISSN 2059-7983 JRNL PMID 27139626 JRNL DOI 10.1107/S2059798316003065 REMARK 2 REMARK 2 RESOLUTION. 2.00 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.8.0107 REMARK 3 AUTHORS : MURSHUDOV,SKUBAK,LEBEDEV,PANNU,STEINER, REMARK 3 : NICHOLLS,WINN,LONG,VAGIN REMARK 3 REMARK 3 REFINEMENT TARGET : MAXIMUM LIKELIHOOD REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.00 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 68.90 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 99.7 REMARK 3 NUMBER OF REFLECTIONS : 30438 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 CROSS-VALIDATION METHOD : THROUGHOUT REMARK 3 FREE R VALUE TEST SET SELECTION : RANDOM REMARK 3 R VALUE (WORKING + TEST SET) : 0.117 REMARK 3 R VALUE (WORKING SET) : 0.115 REMARK 3 FREE R VALUE : 0.154 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.800 REMARK 3 FREE R VALUE TEST SET COUNT : 1540 REMARK 3 REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN. REMARK 3 TOTAL NUMBER OF BINS USED : 20 REMARK 3 BIN RESOLUTION RANGE HIGH (A) : 2.00 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.05 REMARK 3 REFLECTION IN BIN (WORKING SET) : 2238 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 99.74 REMARK 3 BIN R VALUE (WORKING SET) : 0.1100 REMARK 3 BIN FREE R VALUE SET COUNT : 108 REMARK 3 BIN FREE R VALUE : 0.1490 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 3045 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 14 REMARK 3 SOLVENT ATOMS : 509 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 9.71 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -0.06000 REMARK 3 B22 (A**2) : 0.35000 REMARK 3 B33 (A**2) : -0.30000 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : 0.00000 REMARK 3 B23 (A**2) : 0.00000 REMARK 3 REMARK 3 ESTIMATED OVERALL COORDINATE ERROR. REMARK 3 ESU BASED ON R VALUE (A): 0.101 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.109 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.062 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 2.134 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.971 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.944 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 3221 ; 0.023 ; 0.019 REMARK 3 BOND LENGTHS OTHERS (A): 2998 ; 0.002 ; 0.020 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 4369 ; 2.011 ; 1.953 REMARK 3 BOND ANGLES OTHERS (DEGREES): 6868 ; 1.087 ; 3.000 REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 406 ; 5.675 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 179 ;32.531 ;22.570 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 515 ;12.777 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 42 ;16.709 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 450 ; 0.125 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 3765 ; 0.012 ; 0.021 REMARK 3 GENERAL PLANES OTHERS (A): 821 ; 0.003 ; 0.020 REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED CONTACTS OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION OTHERS (A): NULL ; NULL ; NULL REMARK 3 H-BOND (X...Y) REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 H-BOND (X...Y) OTHERS (A): NULL ; NULL ; NULL REMARK 3 POTENTIAL METAL-ION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 POTENTIAL METAL-ION OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY VDW REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY VDW OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY H-BOND REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY H-BOND OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY METAL-ION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY METAL-ION OTHERS (A): NULL ; NULL ; NULL REMARK 3 REMARK 3 ISOTROPIC THERMAL FACTOR RESTRAINTS. COUNT RMS WEIGHT REMARK 3 MAIN-CHAIN BOND REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 LONG RANGE B REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 LONG RANGE B OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 REMARK 3 ANISOTROPIC THERMAL FACTOR RESTRAINTS. COUNT RMS WEIGHT REMARK 3 RIGID-BOND RESTRAINTS (A**2): NULL ; NULL ; NULL REMARK 3 SPHERICITY; FREE ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SPHERICITY; BONDED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 REMARK 3 NCS RESTRAINTS STATISTICS REMARK 3 NUMBER OF DIFFERENT NCS GROUPS : NULL REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : NULL REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : MASK REMARK 3 PARAMETERS FOR MASK CALCULATION REMARK 3 VDW PROBE RADIUS : 1.20 REMARK 3 ION PROBE RADIUS : 0.80 REMARK 3 SHRINKAGE RADIUS : 0.80 REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: HYDROGENS HAVE BEEN ADDED IN THE RIDING REMARK 3 POSITIONS REMARK 4 REMARK 4 4ZB5 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 23-APR-15. REMARK 100 THE DEPOSITION ID IS D_1000208978. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 09-FEB-15 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 7.0 REMARK 200 NUMBER OF CRYSTALS USED : NULL REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : DIAMOND REMARK 200 BEAMLINE : I02 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.9795 REMARK 200 MONOCHROMATOR : SI (111) REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS PILATUS 6M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XIA2 XIA2/DIALS REMARK 200 DATA SCALING SOFTWARE : XIA2 XIA2/DIALS REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 31979 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.000 REMARK 200 RESOLUTION RANGE LOW (A) : 68.900 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.8 REMARK 200 DATA REDUNDANCY : 4.400 REMARK 200 R MERGE (I) : 0.05000 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 18.7000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.00 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.10 REMARK 200 COMPLETENESS FOR SHELL (%) : 99.8 REMARK 200 DATA REDUNDANCY IN SHELL : 4.60 REMARK 200 R MERGE FOR SHELL (I) : 0.06800 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 15.40 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: MOLREP 11.3.01 REMARK 200 STARTING MODEL: 1MNZ REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 54.69 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.71 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.1M HEPES, 10% PEG 400, 0.05 M REMARK 280 MANGANESE CHLORIDE, 20% GLUCOSE, PH 7.0, VAPOR DIFFUSION, REMARK 280 SITTING DROP, TEMPERATURE 293K 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 46.45200 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 49.07600 REMARK 290 SMTRY3 5 0.000000 0.000000 1.000000 51.35200 REMARK 290 SMTRY1 6 -1.000000 0.000000 0.000000 46.45200 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 49.07600 REMARK 290 SMTRY3 6 0.000000 0.000000 1.000000 51.35200 REMARK 290 SMTRY1 7 -1.000000 0.000000 0.000000 46.45200 REMARK 290 SMTRY2 7 0.000000 1.000000 0.000000 49.07600 REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 51.35200 REMARK 290 SMTRY1 8 1.000000 0.000000 0.000000 46.45200 REMARK 290 SMTRY2 8 0.000000 -1.000000 0.000000 49.07600 REMARK 290 SMTRY3 8 0.000000 0.000000 -1.000000 51.35200 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: 33730 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 44860 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -143.0 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 -102.70400 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 -102.70400 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 519 LIES ON A SPECIAL POSITION. REMARK 375 HOH A 898 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 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 505 O HOH A 750 0.90 REMARK 500 O HOH A 858 O HOH A 874 0.97 REMARK 500 O HOH A 713 O HOH A 740 1.02 REMARK 500 O HOH A 649 O HOH A 844 1.18 REMARK 500 O HOH A 581 O HOH A 798 1.24 REMARK 500 O HOH A 604 O HOH A 870 1.32 REMARK 500 O HOH A 765 O HOH A 856 1.45 REMARK 500 O HOH A 940 O HOH A 973 1.55 REMARK 500 O HOH A 980 O HOH A 988 1.67 REMARK 500 O HOH A 973 O HOH A 993 1.68 REMARK 500 O HOH A 826 O HOH A 868 1.69 REMARK 500 O HOH A 811 O HOH A 837 1.73 REMARK 500 O HOH A 630 O HOH A 923 1.79 REMARK 500 O HOH A 753 O HOH A 894 1.83 REMARK 500 O HOH A 946 O HOH A 988 2.03 REMARK 500 OE1 GLU A 328 O HOH A 501 2.12 REMARK 500 OE1 GLU A 328 O HOH A 502 2.12 REMARK 500 O HOH A 506 O HOH A 579 2.15 REMARK 500 O HOH A 563 O HOH A 820 2.16 REMARK 500 OD1 ASP A 376 O HOH A 503 2.16 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 503 O HOH A 719 4554 0.96 REMARK 500 O HOH A 510 O HOH A 853 2555 1.70 REMARK 500 O HOH A 947 O HOH A 961 3554 2.14 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: COVALENT BOND LENGTHS 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,2(A3,1X,A1,I4,A1,1X,A4,3X),1X,F6.3) 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 RES CSSEQI ATM2 DEVIATION REMARK 500 ARG A 74 NE ARG A 74 CZ 0.945 REMARK 500 ARG A 74 NE ARG A 74 CZ 0.080 REMARK 500 ARG A 74 CZ ARG A 74 NH1 0.086 REMARK 500 GLU A 160 CD GLU A 160 OE1 0.115 REMARK 500 GLU A 160 CD GLU A 160 OE2 0.075 REMARK 500 GLU A 207 CD GLU A 207 OE2 0.075 REMARK 500 GLU A 328 CD GLU A 328 OE2 0.108 REMARK 500 GLU A 337 CD GLU A 337 OE2 -0.066 REMARK 500 ARG A 340 CZ ARG A 340 NH2 0.087 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 ASP A 24 CB - CG - OD2 ANGL. DEV. = -5.4 DEGREES REMARK 500 ARG A 74 CD - NE - CZ ANGL. DEV. = -35.6 DEGREES REMARK 500 ARG A 74 NH1 - CZ - NH2 ANGL. DEV. = -10.1 DEGREES REMARK 500 ARG A 74 NE - CZ - NH1 ANGL. DEV. = 4.0 DEGREES REMARK 500 ARG A 74 NE - CZ - NH2 ANGL. DEV. = 9.9 DEGREES REMARK 500 ARG A 74 NE - CZ - NH2 ANGL. DEV. = 6.0 DEGREES REMARK 500 ASP A 110 CB - CG - OD2 ANGL. DEV. = -5.5 DEGREES REMARK 500 ARG A 113 NE - CZ - NH1 ANGL. DEV. = 3.2 DEGREES REMARK 500 ARG A 113 NE - CZ - NH2 ANGL. DEV. = -3.5 DEGREES REMARK 500 GLU A 160 OE1 - CD - OE2 ANGL. DEV. = 7.6 DEGREES REMARK 500 ASP A 245 CB - CG - OD1 ANGL. DEV. = 6.0 DEGREES REMARK 500 ARG A 266 NE - CZ - NH1 ANGL. DEV. = 4.1 DEGREES REMARK 500 ARG A 266 NE - CZ - NH2 ANGL. DEV. = -5.2 DEGREES REMARK 500 ASP A 295 CB - CG - OD1 ANGL. DEV. = 6.3 DEGREES REMARK 500 ASP A 336 CB - CG - OD1 ANGL. DEV. = 5.7 DEGREES REMARK 500 GLU A 337 CG - CD - OE1 ANGL. DEV. = 12.7 DEGREES REMARK 500 GLU A 337 CG - CD - OE2 ANGL. DEV. = -12.3 DEGREES REMARK 500 ARG A 340 NE - CZ - NH1 ANGL. DEV. = -6.0 DEGREES REMARK 500 ARG A 340 NE - CZ - NH2 ANGL. DEV. = 5.8 DEGREES REMARK 500 ARG A 354 NE - CZ - NH1 ANGL. DEV. = 4.3 DEGREES REMARK 500 ARG A 368 NE - CZ - NH1 ANGL. DEV. = -5.1 DEGREES REMARK 500 ARG A 368 NE - CZ - NH2 ANGL. DEV. = -3.6 DEGREES REMARK 500 ARG A 368 NE - CZ - NH2 ANGL. DEV. = 4.3 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 -76.67 -88.49 REMARK 500 PHE A 94 -28.74 -143.28 REMARK 500 GLU A 186 108.20 81.11 REMARK 500 ASN A 247 -168.67 -169.55 REMARK 500 ASN A 250 77.04 -101.93 REMARK 500 LYS A 253 -173.97 -170.52 REMARK 500 TYR A 254 160.16 -49.99 REMARK 500 ALA A 343 65.34 -153.24 REMARK 500 PHE A 357 -73.36 -158.10 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: PLANAR GROUPS REMARK 500 REMARK 500 PLANAR GROUPS IN THE FOLLOWING RESIDUES HAVE A TOTAL REMARK 500 RMS DISTANCE OF ALL ATOMS FROM THE BEST-FIT PLANE REMARK 500 BY MORE THAN AN EXPECTED VALUE OF 6*RMSD, WITH AN REMARK 500 RMSD 0.02 ANGSTROMS, OR AT LEAST ONE ATOM HAS REMARK 500 AN RMSD GREATER THAN THIS VALUE REMARK 500 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 500 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 M RES CSSEQI RMS TYPE REMARK 500 ARG A 74 0.20 SIDE CHAIN REMARK 500 REMARK 500 REMARK: NULL REMARK 525 REMARK 525 SOLVENT REMARK 525 REMARK 525 THE SOLVENT MOLECULES HAVE CHAIN IDENTIFIERS THAT REMARK 525 INDICATE THE POLYMER CHAIN WITH WHICH THEY ARE MOST REMARK 525 CLOSELY ASSOCIATED. THE REMARK LISTS ALL THE SOLVENT REMARK 525 MOLECULES WHICH ARE MORE THAN 5A AWAY FROM THE REMARK 525 NEAREST POLYMER CHAIN (M = MODEL NUMBER; REMARK 525 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE REMARK 525 NUMBER; I=INSERTION CODE): REMARK 525 REMARK 525 M RES CSSEQI REMARK 525 HOH A1009 DISTANCE = 6.11 ANGSTROMS 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 MN A 401 MN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 GLU A 181 OE2 REMARK 620 2 GLU A 217 OE1 95.3 REMARK 620 3 ASP A 245 OD2 92.9 111.4 REMARK 620 4 ASP A 287 OD2 163.8 86.5 101.4 REMARK 620 5 GLC A 403 O4 83.3 166.7 81.9 91.2 REMARK 620 6 GLC A 403 O3 83.4 91.2 157.4 80.4 75.5 REMARK 620 N 1 2 3 4 5 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MN A 402 MN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 GLU A 217 OE2 REMARK 620 2 HIS A 220 NE2 84.1 REMARK 620 3 ASP A 255 OD1 99.5 90.0 REMARK 620 4 ASP A 255 OD2 157.6 91.8 58.5 REMARK 620 5 ASP A 257 OD1 86.3 168.0 84.5 94.3 REMARK 620 6 HOH A 540 O 114.7 108.0 142.4 87.4 82.7 REMARK 620 N 1 2 3 4 5 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 4ZBO RELATED DB: PDB REMARK 900 OTHER STRUCTURES OF GLUCOSE ISOMERASE FROM THIS STUDY REMARK 900 RELATED ID: 4ZB2 RELATED DB: PDB REMARK 900 OTHER STRUCTURES OF GLUCOSE ISOMERASE FROM THIS STUDY DBREF 4ZB5 A 1 387 UNP P24300 XYLA_STRRU 1 387 SEQADV 4ZB5 GLY A 388 UNP P24300 EXPRESSION TAG 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 MN A 401 1 HET MN A 402 1 HET GLC A 403 12 HETNAM MN MANGANESE (II) ION HETNAM GLC ALPHA-D-GLUCOPYRANOSE HETSYN GLC ALPHA-D-GLUCOSE; D-GLUCOSE; GLUCOSE FORMUL 2 MN 2(MN 2+) FORMUL 4 GLC C6 H12 O6 FORMUL 5 HOH *509(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 ALA A 278 1 15 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 OE2 GLU A 181 MN MN A 401 1555 1555 2.13 LINK OE1 GLU A 217 MN MN A 401 1555 1555 2.19 LINK OE2 GLU A 217 MN MN A 402 1555 1555 2.08 LINK NE2 HIS A 220 MN MN A 402 1555 1555 2.37 LINK OD2 ASP A 245 MN MN A 401 1555 1555 2.17 LINK OD1 ASP A 255 MN MN A 402 1555 1555 2.34 LINK OD2 ASP A 255 MN MN A 402 1555 1555 2.23 LINK OD1 ASP A 257 MN MN A 402 1555 1555 2.22 LINK OD2 ASP A 287 MN MN A 401 1555 1555 2.12 LINK MN MN A 401 O4 GLC A 403 1555 1555 2.03 LINK MN MN A 401 O3 GLC A 403 1555 1555 2.21 LINK MN MN A 402 O HOH A 540 1555 1555 2.27 CISPEP 1 GLU A 186 PRO A 187 0 12.77 CRYST1 92.904 98.152 102.704 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 0.010764 0.000000 0.000000 0.00000 SCALE2 0.000000 0.010188 0.000000 0.00000 SCALE3 0.000000 0.000000 0.009737 0.00000