HEADER ISOMERASE 22-OCT-12 4HOW TITLE THE CRYSTAL STRUCTURE OF ISOMALTULOSE SYNTHASE FROM ERWINIA RHAPONTICI TITLE 2 NX5 COMPND MOL_ID: 1; COMPND 2 MOLECULE: SUCROSE ISOMERASE; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: ISOMALTULOSE SYNTHASE; COMPND 5 EC: 5.4.99.11; COMPND 6 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: ERWINIA RHAPONTICI; SOURCE 3 ORGANISM_TAXID: 55212; SOURCE 4 STRAIN: NX5; SOURCE 5 GENE: PALI; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 8 EXPRESSION_SYSTEM_STRAIN: BL21(DE3); SOURCE 9 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 10 EXPRESSION_SYSTEM_PLASMID: PET-22B KEYWDS TIM BARREL, ISOMERASE, HYDROLASE, CALCIUM BINDING EXPDTA X-RAY DIFFRACTION AUTHOR Z.XU,S.LI,H.XU,J.ZHOU REVDAT 2 08-NOV-23 4HOW 1 REMARK LINK REVDAT 1 16-OCT-13 4HOW 0 JRNL AUTH Z.XU,S.LI,J.LI,Y.LI,X.FENG,R.WANG,H.XU,J.ZHOU JRNL TITL THE STRUCTURAL BASIS OF ERWINIA RHAPONTICI ISOMALTULOSE JRNL TITL 2 SYNTHASE JRNL REF PLOS ONE V. 8 74788 2013 JRNL REFN ESSN 1932-6203 JRNL PMID 24069347 JRNL DOI 10.1371/JOURNAL.PONE.0074788 REMARK 2 REMARK 2 RESOLUTION. 1.70 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.6.0117 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) : 1.70 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 45.06 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 98.9 REMARK 3 NUMBER OF REFLECTIONS : 69233 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) : 0.161 REMARK 3 R VALUE (WORKING SET) : 0.159 REMARK 3 FREE R VALUE : 0.193 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.000 REMARK 3 FREE R VALUE TEST SET COUNT : 3669 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) : 1.70 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.74 REMARK 3 REFLECTION IN BIN (WORKING SET) : 4202 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 86.77 REMARK 3 BIN R VALUE (WORKING SET) : 0.3260 REMARK 3 BIN FREE R VALUE SET COUNT : 239 REMARK 3 BIN FREE R VALUE : 0.4170 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 4660 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 19 REMARK 3 SOLVENT ATOMS : 728 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 21.34 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -0.02000 REMARK 3 B22 (A**2) : 0.03000 REMARK 3 B33 (A**2) : -0.01000 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): 0.094 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.094 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.057 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 1.724 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.971 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.959 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 4899 ; 0.026 ; 0.020 REMARK 3 BOND LENGTHS OTHERS (A): NULL ; NULL ; NULL REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 6654 ; 2.252 ; 1.929 REMARK 3 BOND ANGLES OTHERS (DEGREES): NULL ; NULL ; NULL REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 581 ; 6.477 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 279 ;38.014 ;24.194 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 822 ;13.672 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 35 ;15.811 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 668 ; 0.189 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 3899 ; 0.014 ; 0.021 REMARK 3 GENERAL PLANES OTHERS (A): NULL ; NULL ; NULL 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 USED IF PRESENT IN REMARK 3 THE INPUT REMARK 4 REMARK 4 4HOW COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 24-OCT-12. REMARK 100 THE DEPOSITION ID IS D_1000075735. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 21-MAY-12 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 9.0 REMARK 200 NUMBER OF CRYSTALS USED : NULL REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : SSRF REMARK 200 BEAMLINE : BL17U 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 : NULL REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : HKL-2000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 99625 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.700 REMARK 200 RESOLUTION RANGE LOW (A) : 50.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 2.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 70.0 REMARK 200 DATA REDUNDANCY : NULL REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : NULL REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.70 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.76 REMARK 200 COMPLETENESS FOR SHELL (%) : 96.6 REMARK 200 DATA REDUNDANCY IN SHELL : 1.70 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: AMORE REMARK 200 STARTING MODEL: 1M53 REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 47.84 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.36 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 30% PEG 6000, 0.1M BICINE, 10%(W/V) REMARK 280 GLYCEROL, PH 9.0, VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 293K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 21 21 21 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X+1/2,-Y,Z+1/2 REMARK 290 3555 -X,Y+1/2,-Z+1/2 REMARK 290 4555 X+1/2,-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 29.42800 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 68.99900 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 40.63350 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 68.99900 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 29.42800 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 40.63350 REMARK 290 SMTRY3 4 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 ASP A 2 REMARK 465 SER A 3 REMARK 465 GLN A 4 REMARK 465 GLY A 5 REMARK 465 LEU A 6 REMARK 465 LYS A 7 REMARK 465 THR A 8 REMARK 465 ALA A 9 REMARK 465 VAL A 10 REMARK 465 ALA A 11 REMARK 465 ILE A 12 REMARK 465 PHE A 13 REMARK 465 LEU A 14 REMARK 465 ALA A 15 REMARK 465 THR A 16 REMARK 465 THR A 17 REMARK 465 PHE A 18 REMARK 465 SER A 19 REMARK 465 ALA A 20 REMARK 465 THR A 21 REMARK 465 SER A 22 REMARK 465 TYR A 23 REMARK 465 GLN A 24 REMARK 465 ALA A 25 REMARK 465 CYS A 26 REMARK 465 SER A 27 REMARK 465 ALA A 28 REMARK 465 GLY A 29 REMARK 465 PRO A 30 REMARK 465 ASP A 31 REMARK 465 THR A 32 REMARK 465 ALA A 33 REMARK 465 PRO A 34 REMARK 465 SER A 35 REMARK 465 LEU A 36 REMARK 465 THR A 37 REMARK 465 VAL A 38 REMARK 465 GLN A 39 REMARK 465 GLN A 40 REMARK 465 SER A 41 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 1009 O HOH A 1468 1.45 REMARK 500 O HOH A 1445 O HOH A 1509 1.85 REMARK 500 OD1 ASN A 510 O HOH A 1239 1.88 REMARK 500 O HOH A 1510 O HOH A 1522 1.92 REMARK 500 O HOH A 1306 O HOH A 1467 1.92 REMARK 500 O HOH A 1446 O HOH A 1509 2.00 REMARK 500 O HOH A 1447 O HOH A 1498 2.01 REMARK 500 OH TYR A 182 O HOH A 1468 2.05 REMARK 500 O HOH A 1304 O HOH A 1523 2.12 REMARK 500 O HOH A 1009 O HOH A 1248 2.14 REMARK 500 O HOH A 1096 O HOH A 1154 2.15 REMARK 500 O HOH A 1033 O HOH A 1278 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 1360 O HOH A 1480 1455 2.00 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 TRP A 91 CE2 TRP A 91 CD2 0.084 REMARK 500 TYR A 168 CE1 TYR A 168 CZ 0.109 REMARK 500 HIS A 203 CG HIS A 203 CD2 0.059 REMARK 500 TRP A 214 CE2 TRP A 214 CD2 0.085 REMARK 500 GLU A 283 CD GLU A 283 OE2 0.069 REMARK 500 SER A 409 CA SER A 409 CB 0.109 REMARK 500 SER A 409 CB SER A 409 OG 0.140 REMARK 500 TYR A 558 CG TYR A 558 CD1 0.080 REMARK 500 HIS A 576 CG HIS A 576 CD2 0.069 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 59 NE - CZ - NH1 ANGL. DEV. = 3.8 DEGREES REMARK 500 ARG A 59 NE - CZ - NH2 ANGL. DEV. = -3.3 DEGREES REMARK 500 ASP A 106 CB - CG - OD1 ANGL. DEV. = 5.4 DEGREES REMARK 500 ARG A 125 NE - CZ - NH1 ANGL. DEV. = 4.4 DEGREES REMARK 500 ARG A 125 NE - CZ - NH2 ANGL. DEV. = -3.5 DEGREES REMARK 500 ARG A 133 NE - CZ - NH1 ANGL. DEV. = 3.4 DEGREES REMARK 500 ARG A 136 NE - CZ - NH2 ANGL. DEV. = -3.2 DEGREES REMARK 500 ASP A 254 CB - CG - OD1 ANGL. DEV. = 5.6 DEGREES REMARK 500 ASP A 302 CB - CG - OD2 ANGL. DEV. = 5.8 DEGREES REMARK 500 ARG A 333 NE - CZ - NH2 ANGL. DEV. = 3.0 DEGREES REMARK 500 ARG A 385 NE - CZ - NH2 ANGL. DEV. = -5.2 DEGREES REMARK 500 SER A 409 CB - CA - C ANGL. DEV. = 18.6 DEGREES REMARK 500 ASP A 425 CB - CG - OD1 ANGL. DEV. = -6.8 DEGREES REMARK 500 ASP A 425 CB - CG - OD2 ANGL. DEV. = 7.1 DEGREES REMARK 500 ARG A 452 NE - CZ - NH2 ANGL. DEV. = -3.3 DEGREES REMARK 500 ASP A 466 CB - CG - OD1 ANGL. DEV. = 7.7 DEGREES REMARK 500 ASP A 493 CB - CG - OD1 ANGL. DEV. = -7.0 DEGREES REMARK 500 ASP A 493 CB - CG - OD2 ANGL. DEV. = 10.7 DEGREES REMARK 500 ARG A 512 NE - CZ - NH1 ANGL. DEV. = 3.0 DEGREES REMARK 500 ARG A 587 NE - CZ - NH1 ANGL. DEV. = 4.0 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 PHE A 61 -68.24 -93.22 REMARK 500 ASN A 103 56.65 38.54 REMARK 500 ASP A 109 116.07 -163.30 REMARK 500 HIS A 177 -166.21 -126.64 REMARK 500 PHE A 205 -132.61 -100.48 REMARK 500 THR A 242 57.47 35.14 REMARK 500 ASN A 262 56.27 -152.01 REMARK 500 VAL A 284 -59.63 -130.52 REMARK 500 GLU A 314 -101.68 -122.43 REMARK 500 ASN A 367 -169.90 -177.55 REMARK 500 ALA A 471 25.50 48.56 REMARK 500 ASN A 485 0.55 -65.57 REMARK 500 ASP A 527 93.76 -166.16 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 CA A 704 CA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP A 63 OD1 REMARK 620 2 ASN A 65 OD1 79.4 REMARK 620 3 ASP A 67 OD1 88.3 71.7 REMARK 620 4 ILE A 69 O 90.3 156.5 87.1 REMARK 620 5 ASP A 71 OD2 88.9 102.5 173.9 98.4 REMARK 620 6 HOH A 848 O 158.7 79.6 81.5 107.7 99.3 REMARK 620 N 1 2 3 4 5 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE GOL A 701 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE GOL A 702 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE GOL A 703 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CA A 704 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 4HOX RELATED DB: PDB REMARK 900 RELATED ID: 4HOZ RELATED DB: PDB REMARK 900 RELATED ID: 4HP5 RELATED DB: PDB REMARK 900 RELATED ID: 4HPH RELATED DB: PDB DBREF 4HOW A 1 600 UNP D9MPF2 D9MPF2_ERWRD 1 600 SEQRES 1 A 600 MET ASP SER GLN GLY LEU LYS THR ALA VAL ALA ILE PHE SEQRES 2 A 600 LEU ALA THR THR PHE SER ALA THR SER TYR GLN ALA CYS SEQRES 3 A 600 SER ALA GLY PRO ASP THR ALA PRO SER LEU THR VAL GLN SEQRES 4 A 600 GLN SER ASN ALA LEU PRO THR TRP TRP LYS GLN ALA VAL SEQRES 5 A 600 PHE TYR GLN VAL TYR PRO ARG SER PHE LYS ASP THR ASN SEQRES 6 A 600 GLY ASP GLY ILE GLY ASP LEU ASN GLY ILE ILE GLU ASN SEQRES 7 A 600 LEU ASP TYR LEU LYS LYS LEU GLY ILE ASP ALA ILE TRP SEQRES 8 A 600 ILE ASN PRO HIS TYR ASP SER PRO ASN THR ASP ASN GLY SEQRES 9 A 600 TYR ASP ILE ARG ASP TYR ARG LYS ILE MET LYS GLU TYR SEQRES 10 A 600 GLY THR MET GLU ASP PHE ASP ARG LEU ILE SER GLU MET SEQRES 11 A 600 LYS LYS ARG ASN MET ARG LEU MET ILE ASP ILE VAL ILE SEQRES 12 A 600 ASN HIS THR SER ASP GLN HIS ALA TRP PHE VAL GLN SER SEQRES 13 A 600 LYS SER GLY LYS ASN ASN PRO TYR ARG ASP TYR TYR PHE SEQRES 14 A 600 TRP ARG ASP GLY LYS ASP GLY HIS ALA PRO ASN ASN TYR SEQRES 15 A 600 PRO SER PHE PHE GLY GLY SER ALA TRP GLU LYS ASP ASP SEQRES 16 A 600 LYS SER GLY GLN TYR TYR LEU HIS TYR PHE ALA LYS GLN SEQRES 17 A 600 GLN PRO ASP LEU ASN TRP ASP ASN PRO LYS VAL ARG GLN SEQRES 18 A 600 ASP LEU TYR ASP MET LEU ARG PHE TRP LEU ASP LYS GLY SEQRES 19 A 600 VAL SER GLY LEU ARG PHE ASP THR VAL ALA THR TYR SER SEQRES 20 A 600 LYS ILE PRO ASN PHE PRO ASP LEU SER GLN GLN GLN LEU SEQRES 21 A 600 LYS ASN PHE ALA GLU GLU TYR THR LYS GLY PRO LYS ILE SEQRES 22 A 600 HIS ASP TYR VAL ASN GLU MET ASN ARG GLU VAL LEU SER SEQRES 23 A 600 HIS TYR ASP ILE ALA THR ALA GLY GLU ILE PHE GLY VAL SEQRES 24 A 600 PRO LEU ASP LYS SER ILE LYS PHE PHE ASP ARG ARG ARG SEQRES 25 A 600 ASN GLU LEU ASN ILE ALA PHE THR PHE ASP LEU ILE ARG SEQRES 26 A 600 LEU ASP ARG ASP ALA ASP GLU ARG TRP ARG ARG LYS ASP SEQRES 27 A 600 TRP THR LEU SER GLN PHE ARG LYS ILE VAL ASP LYS VAL SEQRES 28 A 600 ASP GLN THR ALA GLY GLU TYR GLY TRP ASN ALA PHE PHE SEQRES 29 A 600 LEU ASP ASN HIS ASP ASN PRO ARG ALA VAL SER HIS PHE SEQRES 30 A 600 GLY ASP ASP ARG PRO GLN TRP ARG GLU HIS ALA ALA LYS SEQRES 31 A 600 ALA LEU ALA THR LEU THR LEU THR GLN ARG ALA THR PRO SEQRES 32 A 600 PHE ILE TYR GLN GLY SER GLU LEU GLY MET THR ASN TYR SEQRES 33 A 600 PRO PHE LYS LYS ILE ASP ASP PHE ASP ASP VAL GLU VAL SEQRES 34 A 600 LYS GLY PHE TRP GLN ASP TYR VAL GLU THR GLY LYS VAL SEQRES 35 A 600 LYS ALA GLU GLU PHE LEU GLN ASN VAL ARG GLN THR SER SEQRES 36 A 600 ARG ASP ASN SER ARG THR PRO PHE GLN TRP ASP ALA SER SEQRES 37 A 600 LYS ASN ALA GLY PHE THR SER GLY THR PRO TRP LEU LYS SEQRES 38 A 600 ILE ASN PRO ASN TYR LYS GLU ILE ASN SER ALA ASP GLN SEQRES 39 A 600 ILE ASN ASN PRO ASN SER VAL PHE ASN TYR TYR ARG LYS SEQRES 40 A 600 LEU ILE ASN ILE ARG HIS ASP ILE PRO ALA LEU THR TYR SEQRES 41 A 600 GLY SER TYR ILE ASP LEU ASP PRO ASP ASN ASN SER VAL SEQRES 42 A 600 TYR ALA TYR THR ARG THR LEU GLY ALA GLU LYS TYR LEU SEQRES 43 A 600 VAL VAL ILE ASN PHE LYS GLU GLU VAL MET HIS TYR THR SEQRES 44 A 600 LEU PRO GLY ASP LEU SER ILE ASN LYS VAL ILE THR GLU SEQRES 45 A 600 ASN ASN SER HIS THR ILE VAL ASN LYS ASN ASP ARG GLN SEQRES 46 A 600 LEU ARG LEU GLU PRO TRP GLN SER GLY ILE TYR LYS LEU SEQRES 47 A 600 ASN PRO HET GOL A 701 6 HET GOL A 702 6 HET GOL A 703 6 HET CA A 704 1 HETNAM GOL GLYCEROL HETNAM CA CALCIUM ION HETSYN GOL GLYCERIN; PROPANE-1,2,3-TRIOL FORMUL 2 GOL 3(C3 H8 O3) FORMUL 5 CA CA 2+ FORMUL 6 HOH *728(H2 O) HELIX 1 1 TYR A 57 PHE A 61 5 5 HELIX 2 2 ASP A 71 ASN A 78 1 8 HELIX 3 3 ASN A 78 GLY A 86 1 9 HELIX 4 4 LYS A 115 GLY A 118 5 4 HELIX 5 5 THR A 119 ARG A 133 1 15 HELIX 6 6 HIS A 150 GLY A 159 1 10 HELIX 7 7 TYR A 164 TYR A 168 5 5 HELIX 8 8 ASN A 216 ASP A 232 1 17 HELIX 9 9 THR A 242 TYR A 246 5 5 HELIX 10 10 GLN A 258 ASN A 262 5 5 HELIX 11 11 PHE A 263 THR A 268 1 6 HELIX 12 12 LYS A 272 VAL A 284 1 13 HELIX 13 13 LEU A 285 TYR A 288 5 4 HELIX 14 14 PRO A 300 LYS A 303 5 4 HELIX 15 15 SER A 304 ASP A 309 1 6 HELIX 16 16 ARG A 310 ASN A 313 5 4 HELIX 17 17 THR A 340 GLY A 356 1 17 HELIX 18 18 ARG A 372 PHE A 377 1 6 HELIX 19 19 TRP A 384 LEU A 397 1 14 HELIX 20 20 GLY A 408 GLY A 412 5 5 HELIX 21 21 LYS A 420 PHE A 424 5 5 HELIX 22 22 ASP A 426 VAL A 437 1 12 HELIX 23 23 LYS A 443 SER A 455 1 13 HELIX 24 24 ARG A 456 ARG A 460 5 5 HELIX 25 25 SER A 468 PHE A 473 5 6 HELIX 26 26 ASN A 483 GLU A 488 5 6 HELIX 27 27 ASN A 490 ILE A 495 1 6 HELIX 28 28 SER A 500 ILE A 515 1 16 HELIX 29 29 PRO A 516 GLY A 521 1 6 SHEET 1 A 8 ILE A 317 PHE A 319 0 SHEET 2 A 8 ALA A 291 GLU A 295 1 N THR A 292 O ILE A 317 SHEET 3 A 8 GLY A 237 PHE A 240 1 N PHE A 240 O ALA A 293 SHEET 4 A 8 ARG A 136 ILE A 141 1 N ILE A 141 O ARG A 239 SHEET 5 A 8 ALA A 89 ILE A 92 1 N ILE A 90 O MET A 138 SHEET 6 A 8 PHE A 53 VAL A 56 1 N VAL A 56 O TRP A 91 SHEET 7 A 8 THR A 402 TYR A 406 1 O ILE A 405 N PHE A 53 SHEET 8 A 8 ALA A 362 PHE A 363 1 N PHE A 363 O PHE A 404 SHEET 1 B 2 TYR A 96 ASP A 97 0 SHEET 2 B 2 ASP A 109 ILE A 113 -1 O LYS A 112 N ASP A 97 SHEET 1 C 3 TRP A 170 ASP A 172 0 SHEET 2 C 3 GLN A 199 LEU A 202 -1 O TYR A 200 N ARG A 171 SHEET 3 C 3 TRP A 191 LYS A 193 -1 N GLU A 192 O TYR A 201 SHEET 1 D 5 SER A 522 ASP A 525 0 SHEET 2 D 5 VAL A 533 LEU A 540 -1 O THR A 539 N SER A 522 SHEET 3 D 5 GLU A 543 ASN A 550 -1 O ILE A 549 N TYR A 534 SHEET 4 D 5 SER A 593 LEU A 598 -1 O LEU A 598 N LYS A 544 SHEET 5 D 5 ILE A 566 ASN A 573 -1 N LYS A 568 O LYS A 597 SHEET 1 E 2 MET A 556 THR A 559 0 SHEET 2 E 2 GLN A 585 LEU A 588 -1 O LEU A 588 N MET A 556 LINK OD1 ASP A 63 CA CA A 704 1555 1555 2.34 LINK OD1 ASN A 65 CA CA A 704 1555 1555 2.57 LINK OD1 ASP A 67 CA CA A 704 1555 1555 2.49 LINK O ILE A 69 CA CA A 704 1555 1555 2.29 LINK OD2 ASP A 71 CA CA A 704 1555 1555 2.46 LINK CA CA A 704 O HOH A 848 1555 1555 2.47 SITE 1 AC1 7 GLU A 295 ARG A 325 ASP A 369 GLU A 428 SITE 2 AC1 7 ARG A 456 GOL A 702 HOH A 886 SITE 1 AC2 9 ASP A 102 TYR A 105 HIS A 145 PHE A 186 SITE 2 AC2 9 PHE A 205 ASP A 241 ARG A 456 GOL A 701 SITE 3 AC2 9 HOH A 886 SITE 1 AC3 5 ILE A 524 LEU A 526 THR A 537 LYS A 544 SITE 2 AC3 5 HOH A1138 SITE 1 AC4 6 ASP A 63 ASN A 65 ASP A 67 ILE A 69 SITE 2 AC4 6 ASP A 71 HOH A 848 CRYST1 58.856 81.267 137.998 90.00 90.00 90.00 P 21 21 21 4 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 0.016991 0.000000 0.000000 0.00000 SCALE2 0.000000 0.012305 0.000000 0.00000 SCALE3 0.000000 0.000000 0.007246 0.00000