HEADER UNKNOWN FUNCTION 31-AUG-04 1XBV
TITLE CRYSTAL STRUCTURE OF 3-KETO-L-GULONATE 6-PHOSPHATE
TITLE 2 DECARBOXYLASE WITH BOUND D-RIBULOSE 5-PHOSPHATE
COMPND MOL_ID: 1;
COMPND 2 MOLECULE: 3-KETO-L-GULONATE 6-PHOSPHATE DECARBOXYLASE;
COMPND 3 CHAIN: A, B;
COMPND 4 ENGINEERED: YES
SOURCE MOL_ID: 1;
SOURCE 2 ORGANISM_SCIENTIFIC: ESCHERICHIA COLI;
SOURCE 3 ORGANISM_TAXID: 562;
SOURCE 4 GENE: ULAD;
SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI;
SOURCE 6 EXPRESSION_SYSTEM_TAXID: 562
KEYWDS BETA/ALPHA BARREL, TIM BARREL, UNKNOWN FUNCTION
EXPDTA X-RAY DIFFRACTION
AUTHOR E.L.WISE,W.S.YEW,J.AKANA,J.A.GERLT,I.RAYMENT
REVDAT 2 24-FEB-09 1XBV 1 VERSN
REVDAT 1 26-APR-05 1XBV 0
JRNL AUTH E.L.WISE,W.S.YEW,J.AKANA,J.A.GERLT,I.RAYMENT
JRNL TITL EVOLUTION OF ENZYMATIC ACTIVITIES IN THE OROTIDINE
JRNL TITL 2 5'-MONOPHOSPHATE DECARBOXYLASE SUPRAFAMILY:
JRNL TITL 3 STRUCTURAL BASIS FOR CATALYTIC PROMISCUITY IN
JRNL TITL 4 WILD-TYPE AND DESIGNED MUTANTS OF
JRNL TITL 5 3-KETO-L-GULONATE 6-PHOSPHATE DECARBOXYLASE
JRNL REF BIOCHEMISTRY V. 44 1816 2005
JRNL REFN ISSN 0006-2960
JRNL PMID 15697207
JRNL DOI 10.1021/BI0478143
REMARK 1
REMARK 2
REMARK 2 RESOLUTION. 1.66 ANGSTROMS.
REMARK 3
REMARK 3 REFINEMENT.
REMARK 3 PROGRAM : REFMAC 5.1.24
REMARK 3 AUTHORS : MURSHUDOV,VAGIN,DODSON
REMARK 3
REMARK 3 REFINEMENT TARGET : ENGH & HUBER
REMARK 3
REMARK 3 DATA USED IN REFINEMENT.
REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.66
REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 91.29
REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000
REMARK 3 COMPLETENESS FOR RANGE (%) : 99.1
REMARK 3 NUMBER OF REFLECTIONS : 51641
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) : 0.164
REMARK 3 R VALUE (WORKING SET) : 0.162
REMARK 3 FREE R VALUE : 0.194
REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.100
REMARK 3 FREE R VALUE TEST SET COUNT : 2762
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) : 1.66
REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.70
REMARK 3 REFLECTION IN BIN (WORKING SET) : 3633
REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : NULL
REMARK 3 BIN R VALUE (WORKING SET) : 0.2800
REMARK 3 BIN FREE R VALUE SET COUNT : 192
REMARK 3 BIN FREE R VALUE : 0.3110
REMARK 3
REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT.
REMARK 3 PROTEIN ATOMS : 3286
REMARK 3 NUCLEIC ACID ATOMS : 0
REMARK 3 HETEROGEN ATOMS : 28
REMARK 3 SOLVENT ATOMS : 425
REMARK 3
REMARK 3 B VALUES.
REMARK 3 FROM WILSON PLOT (A**2) : NULL
REMARK 3 MEAN B VALUE (OVERALL, A**2) : 20.56
REMARK 3 OVERALL ANISOTROPIC B VALUE.
REMARK 3 B11 (A**2) : -0.47000
REMARK 3 B22 (A**2) : 1.39000
REMARK 3 B33 (A**2) : -0.73000
REMARK 3 B12 (A**2) : 0.00000
REMARK 3 B13 (A**2) : 0.83000
REMARK 3 B23 (A**2) : 0.00000
REMARK 3
REMARK 3 ESTIMATED OVERALL COORDINATE ERROR.
REMARK 3 ESU BASED ON R VALUE (A): 0.088
REMARK 3 ESU BASED ON FREE R VALUE (A): 0.088
REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.059
REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 1.771
REMARK 3
REMARK 3 CORRELATION COEFFICIENTS.
REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.969
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): 3369 ; 0.018 ; 0.021
REMARK 3 BOND LENGTHS OTHERS (A): 3147 ; 0.003 ; 0.020
REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 4570 ; 1.648 ; 1.946
REMARK 3 BOND ANGLES OTHERS (DEGREES): 7269 ; 1.152 ; 3.000
REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 425 ; 6.302 ; 5.000
REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): NULL ; NULL ; NULL
REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): NULL ; NULL ; NULL
REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): NULL ; NULL ; NULL
REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 526 ; 0.107 ; 0.200
REMARK 3 GENERAL PLANES REFINED ATOMS (A): 3755 ; 0.007 ; 0.020
REMARK 3 GENERAL PLANES OTHERS (A): 679 ; 0.003 ; 0.020
REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): 719 ; 0.236 ; 0.200
REMARK 3 NON-BONDED CONTACTS OTHERS (A): 3672 ; 0.251 ; 0.200
REMARK 3 NON-BONDED TORSION REFINED ATOMS (A): NULL ; NULL ; NULL
REMARK 3 NON-BONDED TORSION OTHERS (A): 1991 ; 0.084 ; 0.200
REMARK 3 H-BOND (X...Y) REFINED ATOMS (A): 296 ; 0.186 ; 0.200
REMARK 3 H-BOND (X...Y) OTHERS (A): NULL ; NULL ; NULL
REMARK 3 POTENTIAL METAL-ION REFINED ATOMS (A): 3 ; 0.105 ; 0.200
REMARK 3 POTENTIAL METAL-ION OTHERS (A): NULL ; NULL ; NULL
REMARK 3 SYMMETRY VDW REFINED ATOMS (A): 8 ; 0.101 ; 0.200
REMARK 3 SYMMETRY VDW OTHERS (A): 52 ; 0.301 ; 0.200
REMARK 3 SYMMETRY H-BOND REFINED ATOMS (A): 29 ; 0.197 ; 0.200
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): 2115 ; 1.719 ; 2.500
REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL
REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 3379 ; 2.725 ; 4.000
REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 1254 ; 3.773 ; 5.000
REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 1191 ; 5.496 ; 6.500
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 : BABINET MODEL WITH MASK
REMARK 3 PARAMETERS FOR MASK CALCULATION
REMARK 3 VDW PROBE RADIUS : 1.40
REMARK 3 ION PROBE RADIUS : 0.80
REMARK 3 SHRINKAGE RADIUS : 0.80
REMARK 3
REMARK 3 OTHER REFINEMENT REMARKS: NULL
REMARK 4
REMARK 4 1XBV COMPLIES WITH FORMAT V. 3.15, 01-DEC-08
REMARK 100
REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 16-SEP-04.
REMARK 100 THE RCSB ID CODE IS RCSB030181.
REMARK 200
REMARK 200 EXPERIMENTAL DETAILS
REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION
REMARK 200 DATE OF DATA COLLECTION : 01-APR-04
REMARK 200 TEMPERATURE (KELVIN) : 100
REMARK 200 PH : 7.5
REMARK 200 NUMBER OF CRYSTALS USED : 1
REMARK 200
REMARK 200 SYNCHROTRON (Y/N) : Y
REMARK 200 RADIATION SOURCE : APS
REMARK 200 BEAMLINE : 19-ID
REMARK 200 X-RAY GENERATOR MODEL : NULL
REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M
REMARK 200 WAVELENGTH OR RANGE (A) : 0.961
REMARK 200 MONOCHROMATOR : NULL
REMARK 200 OPTICS : NULL
REMARK 200
REMARK 200 DETECTOR TYPE : CCD
REMARK 200 DETECTOR MANUFACTURER : CUSTOM-MADE
REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000
REMARK 200 DATA SCALING SOFTWARE : SCALEPACK
REMARK 200
REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 382817
REMARK 200 RESOLUTION RANGE HIGH (A) : 1.660
REMARK 200 RESOLUTION RANGE LOW (A) : 92.000
REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 2.000
REMARK 200
REMARK 200 OVERALL.
REMARK 200 COMPLETENESS FOR RANGE (%) : 99.1
REMARK 200 DATA REDUNDANCY : NULL
REMARK 200 R MERGE (I) : 0.04200
REMARK 200 R SYM (I) : NULL
REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 15.8000
REMARK 200
REMARK 200 IN THE HIGHEST RESOLUTION SHELL.
REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.66
REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.72
REMARK 200 COMPLETENESS FOR SHELL (%) : 98.2
REMARK 200 DATA REDUNDANCY IN SHELL : NULL
REMARK 200 R MERGE FOR SHELL (I) : 0.43770
REMARK 200 R SYM FOR SHELL (I) : NULL
REMARK 200 <I/SIGMA(I)> FOR SHELL : 3.300
REMARK 200
REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH
REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT
REMARK 200 SOFTWARE USED: MOLREP
REMARK 200 STARTING MODEL: NULL
REMARK 200
REMARK 200 REMARK: NULL
REMARK 280
REMARK 280 CRYSTAL
REMARK 280 SOLVENT CONTENT, VS (%): 50.00
REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.50
REMARK 280
REMARK 280 CRYSTALLIZATION CONDITIONS: 16% PEG 5000 METHYL ETHER, 100 MM
REMARK 280 BTP, 5 MM MGCL2, PH 7.5, VAPOR DIFFUSION, SITTING DROP,
REMARK 280 TEMPERATURE 298K
REMARK 290
REMARK 290 CRYSTALLOGRAPHIC SYMMETRY
REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: C 1 2 1
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+1/2,Y+1/2,Z
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 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 61.90700
REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 20.73550
REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 0.00000
REMARK 290 SMTRY1 4 -1.000000 0.000000 0.000000 61.90700
REMARK 290 SMTRY2 4 0.000000 1.000000 0.000000 20.73550
REMARK 290 SMTRY3 4 0.000000 0.000000 -1.000000 0.00000
REMARK 290
REMARK 290 REMARK: NULL
REMARK 300
REMARK 300 BIOMOLECULE: 1, 2
REMARK 300 SEE REMARK 350 FOR THE AUTHOR PROVIDED AND/OR PROGRAM
REMARK 300 GENERATED ASSEMBLY INFORMATION FOR THE STRUCTURE IN
REMARK 300 THIS ENTRY. THE REMARK MAY ALSO PROVIDE INFORMATION ON
REMARK 300 BURIED SURFACE AREA.
REMARK 350
REMARK 350 COORDINATES FOR A COMPLETE MULTIMER REPRESENTING THE KNOWN
REMARK 350 BIOLOGICALLY SIGNIFICANT OLIGOMERIZATION STATE OF THE
REMARK 350 MOLECULE CAN BE GENERATED BY APPLYING BIOMT TRANSFORMATIONS
REMARK 350 GIVEN BELOW. BOTH NON-CRYSTALLOGRAPHIC AND
REMARK 350 CRYSTALLOGRAPHIC OPERATIONS ARE GIVEN.
REMARK 350
REMARK 350 BIOMOLECULE: 1
REMARK 350 AUTHOR DETERMINED BIOLOGICAL UNIT: DIMERIC
REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC
REMARK 350 SOFTWARE USED: PISA
REMARK 350 TOTAL BURIED SURFACE AREA: 4210 ANGSTROM**2
REMARK 350 SURFACE AREA OF THE COMPLEX: 16030 ANGSTROM**2
REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -39.0 KCAL/MOL
REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, B
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
REMARK 350 BIOMOLECULE: 2
REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: TETRAMERIC
REMARK 350 SOFTWARE USED: PISA
REMARK 350 TOTAL BURIED SURFACE AREA: 10770 ANGSTROM**2
REMARK 350 SURFACE AREA OF THE COMPLEX: 29710 ANGSTROM**2
REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -85.0 KCAL/MOL
REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, B
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 123.81400
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 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 689 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 SER A 2
REMARK 465 GLY A 216
REMARK 465 MET B 1
REMARK 470
REMARK 470 MISSING ATOM
REMARK 470 THE FOLLOWING RESIDUES HAVE MISSING ATOMS(M=MODEL NUMBER;
REMARK 470 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER;
REMARK 470 I=INSERTION CODE):
REMARK 470 M RES CSSEQI ATOMS
REMARK 470 SER B 2 OG
REMARK 470 THR B 114 OG1 CG2
REMARK 470 TYR B 116 CG CD1 CD2 CE1 CE2 CZ OH
REMARK 470 GLU B 120 CG CD OE1 OE2
REMARK 470 GLU B 150 CG CD OE1 OE2
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 OXT GLY B 216 O HOH B 821 1.79
REMARK 500 O HOH B 714 O HOH B 820 1.86
REMARK 500 O HOH B 761 O HOH B 820 2.07
REMARK 500 OE1 GLU B 202 O HOH B 820 2.09
REMARK 500 O HOH B 688 O HOH B 815 2.18
REMARK 500
REMARK 500 REMARK: NULL
REMARK 500
REMARK 500 GEOMETRY AND STEREOCHEMISTRY
REMARK 500 SUBTOPIC: CLOSE CONTACTS
REMARK 500
REMARK 500 THE FOLLOWING ATOMS THAT ARE RELATED BY CRYSTALLOGRAPHIC
REMARK 500 SYMMETRY ARE IN CLOSE CONTACT. AN ATOM LOCATED WITHIN 0.15
REMARK 500 ANGSTROMS OF A SYMMETRY RELATED ATOM IS ASSUMED TO BE ON A
REMARK 500 SPECIAL POSITION AND IS, THEREFORE, LISTED IN REMARK 375
REMARK 500 INSTEAD OF REMARK 500. ATOMS WITH NON-BLANK ALTERNATE
REMARK 500 LOCATION INDICATORS ARE NOT INCLUDED IN THE CALCULATIONS.
REMARK 500
REMARK 500 DISTANCE CUTOFF:
REMARK 500 2.2 ANGSTROMS FOR CONTACTS NOT INVOLVING HYDROGEN ATOMS
REMARK 500 1.6 ANGSTROMS FOR CONTACTS INVOLVING HYDROGEN ATOMS
REMARK 500
REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI SSYMOP DISTANCE
REMARK 500 NZ LYS A 70 OE1 GLU B 104 1545 2.17
REMARK 500 O HOH B 688 O HOH B 812 4545 2.19
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 SER B 2 C LEU B 3 N 0.170
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 23 NE - CZ - NH1 ANGL. DEV. = 4.8 DEGREES
REMARK 500 ASP A 82 CB - CG - OD2 ANGL. DEV. = 6.3 DEGREES
REMARK 500 SER B 2 O - C - N ANGL. DEV. = -20.0 DEGREES
REMARK 500 ASP B 16 CB - CG - OD2 ANGL. DEV. = 5.5 DEGREES
REMARK 500 ASP B 30 CB - CG - OD2 ANGL. DEV. = 5.4 DEGREES
REMARK 500 ASP B 91 CB - CG - OD2 ANGL. DEV. = 5.5 DEGREES
REMARK 500 ARG B 139 NE - CZ - NH2 ANGL. DEV. = -3.2 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 ASN A 80 20.49 80.04
REMARK 500 ASP B 11 47.70 -97.06
REMARK 500
REMARK 500 REMARK: NULL
REMARK 500
REMARK 500 GEOMETRY AND STEREOCHEMISTRY
REMARK 500 SUBTOPIC: MAIN CHAIN PLANARITY
REMARK 500
REMARK 500 THE FOLLOWING RESIDUES HAVE A PSEUDO PLANARITY
REMARK 500 TORSION, C(I) - CA(I) - N(I+1) - O(I), GREATER
REMARK 500 10.0 DEGREES. (M=MODEL NUMBER; RES=RESIDUE NAME;
REMARK 500 C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER;
REMARK 500 I=INSERTION CODE).
REMARK 500
REMARK 500 M RES CSSEQI ANGLE
REMARK 500 SER B 2 28.02
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 B 756 DISTANCE = 5.12 ANGSTROMS
REMARK 525 HOH B 817 DISTANCE = 6.69 ANGSTROMS
REMARK 525 HOH B 819 DISTANCE = 5.06 ANGSTROMS
REMARK 610
REMARK 610 MISSING HETEROATOM
REMARK 610 THE FOLLOWING RESIDUES HAVE MISSING ATOMS (M=MODEL NUMBER;
REMARK 610 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER;
REMARK 610 I=INSERTION CODE):
REMARK 610 M RES C SSEQI
REMARK 610 5RP A 501
REMARK 610 5RP B 502
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 MG A 601 MG
REMARK 620 N RES CSSEQI ATOM
REMARK 620 1 ASP A 62 OD2
REMARK 620 2 5RP A 501 O4 101.5
REMARK 620 3 GLU A 33 OE2 92.5 165.0
REMARK 620 4 HOH A 801 O 109.7 88.0 82.1
REMARK 620 5 HOH A 804 O 90.7 85.9 99.4 159.4
REMARK 620 6 5RP A 501 O13 170.5 74.6 92.4 79.0 80.4
REMARK 620 N 1 2 3 4 5
REMARK 620
REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL
REMARK 620 MG B 602 MG
REMARK 620 N RES CSSEQI ATOM
REMARK 620 1 HOH B 804 O
REMARK 620 2 5RP B 502 O4 87.3
REMARK 620 3 HOH B 809 O 153.7 82.7
REMARK 620 4 GLU B 33 OE2 85.7 165.6 98.2
REMARK 620 5 ASP B 62 OD2 117.2 98.4 88.4 95.9
REMARK 620 6 5RP B 502 O13 78.2 75.1 75.7 91.2 163.4
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 5RP A 501
REMARK 800 SITE_IDENTIFIER: AC2
REMARK 800 EVIDENCE_CODE: SOFTWARE
REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE 5RP B 502
REMARK 800 SITE_IDENTIFIER: AC3
REMARK 800 EVIDENCE_CODE: SOFTWARE
REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MG A 601
REMARK 800 SITE_IDENTIFIER: AC4
REMARK 800 EVIDENCE_CODE: SOFTWARE
REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MG B 602
DBREF 1XBV A 1 216 UNP P39304 ULAD_ECOLI 1 216
DBREF 1XBV B 1 216 UNP P39304 ULAD_ECOLI 1 216
SEQRES 1 A 216 MET SER LEU PRO MET LEU GLN VAL ALA LEU ASP ASN GLN
SEQRES 2 A 216 THR MET ASP SER ALA TYR GLU THR THR ARG LEU ILE ALA
SEQRES 3 A 216 GLU GLU VAL ASP ILE ILE GLU VAL GLY THR ILE LEU CYS
SEQRES 4 A 216 VAL GLY GLU GLY VAL ARG ALA VAL ARG ASP LEU LYS ALA
SEQRES 5 A 216 LEU TYR PRO HIS LYS ILE VAL LEU ALA ASP ALA LYS ILE
SEQRES 6 A 216 ALA ASP ALA GLY LYS ILE LEU SER ARG MET CYS PHE GLU
SEQRES 7 A 216 ALA ASN ALA ASP TRP VAL THR VAL ILE CYS CYS ALA ASP
SEQRES 8 A 216 ILE ASN THR ALA LYS GLY ALA LEU ASP VAL ALA LYS GLU
SEQRES 9 A 216 PHE ASN GLY ASP VAL GLN ILE GLU LEU THR GLY TYR TRP
SEQRES 10 A 216 THR TRP GLU GLN ALA GLN GLN TRP ARG ASP ALA GLY ILE
SEQRES 11 A 216 GLY GLN VAL VAL TYR HIS ARG SER ARG ASP ALA GLN ALA
SEQRES 12 A 216 ALA GLY VAL ALA TRP GLY GLU ALA ASP ILE THR ALA ILE
SEQRES 13 A 216 LYS ARG LEU SER ASP MET GLY PHE LYS VAL THR VAL THR
SEQRES 14 A 216 GLY GLY LEU ALA LEU GLU ASP LEU PRO LEU PHE LYS GLY
SEQRES 15 A 216 ILE PRO ILE HIS VAL PHE ILE ALA GLY ARG SER ILE ARG
SEQRES 16 A 216 ASP ALA ALA SER PRO VAL GLU ALA ALA ARG GLN PHE LYS
SEQRES 17 A 216 ARG SER ILE ALA GLU LEU TRP GLY
SEQRES 1 B 216 MET SER LEU PRO MET LEU GLN VAL ALA LEU ASP ASN GLN
SEQRES 2 B 216 THR MET ASP SER ALA TYR GLU THR THR ARG LEU ILE ALA
SEQRES 3 B 216 GLU GLU VAL ASP ILE ILE GLU VAL GLY THR ILE LEU CYS
SEQRES 4 B 216 VAL GLY GLU GLY VAL ARG ALA VAL ARG ASP LEU LYS ALA
SEQRES 5 B 216 LEU TYR PRO HIS LYS ILE VAL LEU ALA ASP ALA LYS ILE
SEQRES 6 B 216 ALA ASP ALA GLY LYS ILE LEU SER ARG MET CYS PHE GLU
SEQRES 7 B 216 ALA ASN ALA ASP TRP VAL THR VAL ILE CYS CYS ALA ASP
SEQRES 8 B 216 ILE ASN THR ALA LYS GLY ALA LEU ASP VAL ALA LYS GLU
SEQRES 9 B 216 PHE ASN GLY ASP VAL GLN ILE GLU LEU THR GLY TYR TRP
SEQRES 10 B 216 THR TRP GLU GLN ALA GLN GLN TRP ARG ASP ALA GLY ILE
SEQRES 11 B 216 GLY GLN VAL VAL TYR HIS ARG SER ARG ASP ALA GLN ALA
SEQRES 12 B 216 ALA GLY VAL ALA TRP GLY GLU ALA ASP ILE THR ALA ILE
SEQRES 13 B 216 LYS ARG LEU SER ASP MET GLY PHE LYS VAL THR VAL THR
SEQRES 14 B 216 GLY GLY LEU ALA LEU GLU ASP LEU PRO LEU PHE LYS GLY
SEQRES 15 B 216 ILE PRO ILE HIS VAL PHE ILE ALA GLY ARG SER ILE ARG
SEQRES 16 B 216 ASP ALA ALA SER PRO VAL GLU ALA ALA ARG GLN PHE LYS
SEQRES 17 B 216 ARG SER ILE ALA GLU LEU TRP GLY
HET 5RP A 501 13
HET 5RP B 502 13
HET MG A 601 1
HET MG B 602 1
HETNAM 5RP RIBULOSE-5-PHOSPHATE
HETNAM MG MAGNESIUM ION
FORMUL 3 5RP 2(C5 H11 O8 P)
FORMUL 5 MG 2(MG 2+)
FORMUL 7 HOH *425(H2 O)
HELIX 1 1 THR A 14 ALA A 26 1 13
HELIX 2 2 GLU A 27 VAL A 29 5 3
HELIX 3 3 GLY A 35 GLY A 43 1 9
HELIX 4 4 VAL A 44 TYR A 54 1 11
HELIX 5 5 ALA A 68 ALA A 79 1 12
HELIX 6 6 ASP A 91 PHE A 105 1 15
HELIX 7 7 THR A 118 GLY A 129 1 12
HELIX 8 8 SER A 138 ALA A 144 1 7
HELIX 9 9 GLY A 149 MET A 162 1 14
HELIX 10 10 ALA A 173 LYS A 181 5 9
HELIX 11 11 GLY A 191 ASP A 196 1 6
HELIX 12 12 SER A 199 TRP A 215 1 17
HELIX 13 13 THR B 14 ALA B 26 1 13
HELIX 14 14 GLY B 35 GLY B 43 1 9
HELIX 15 15 VAL B 44 TYR B 54 1 11
HELIX 16 16 ALA B 68 ALA B 79 1 12
HELIX 17 17 ASP B 91 PHE B 105 1 15
HELIX 18 18 THR B 118 GLY B 129 1 12
HELIX 19 19 SER B 138 ALA B 144 1 7
HELIX 20 20 GLY B 149 MET B 162 1 14
HELIX 21 21 ALA B 173 LYS B 181 5 9
HELIX 22 22 GLY B 191 ASP B 196 1 6
HELIX 23 23 SER B 199 GLY B 216 1 18
SHEET 1 A 9 MET A 5 LEU A 10 0
SHEET 2 A 9 ILE A 31 VAL A 34 1 O GLU A 33 N VAL A 8
SHEET 3 A 9 ILE A 58 ILE A 65 1 O LEU A 60 N VAL A 34
SHEET 4 A 9 TRP A 83 ILE A 87 1 O TRP A 83 N ALA A 61
SHEET 5 A 9 ASP A 108 LEU A 113 1 O GLU A 112 N VAL A 86
SHEET 6 A 9 GLN A 132 HIS A 136 1 O VAL A 134 N ILE A 111
SHEET 7 A 9 LYS A 165 THR A 169 1 O THR A 167 N TYR A 135
SHEET 8 A 9 VAL A 187 ALA A 190 1 O ILE A 189 N VAL A 168
SHEET 9 A 9 MET A 5 LEU A 10 1 N MET A 5 O PHE A 188
SHEET 1 B 9 MET B 5 LEU B 10 0
SHEET 2 B 9 ILE B 31 VAL B 34 1 O GLU B 33 N VAL B 8
SHEET 3 B 9 ILE B 58 ILE B 65 1 O LEU B 60 N VAL B 34
SHEET 4 B 9 TRP B 83 ILE B 87 1 O TRP B 83 N ALA B 61
SHEET 5 B 9 ASP B 108 LEU B 113 1 O GLU B 112 N VAL B 86
SHEET 6 B 9 GLN B 132 HIS B 136 1 O VAL B 134 N ILE B 111
SHEET 7 B 9 LYS B 165 THR B 169 1 O THR B 167 N TYR B 135
SHEET 8 B 9 VAL B 187 ALA B 190 1 O VAL B 187 N VAL B 168
SHEET 9 B 9 MET B 5 LEU B 10 1 N GLN B 7 O ALA B 190
SSBOND 1 CYS A 89 CYS B 89 1555 1555 2.12
LINK MG MG A 601 OD2 ASP A 62 1555 1555 2.01
LINK MG MG A 601 O4 5RP A 501 1555 1555 2.11
LINK MG MG A 601 OE2 GLU A 33 1555 1555 2.02
LINK MG MG A 601 O HOH A 801 1555 1555 2.09
LINK MG MG A 601 O HOH A 804 1555 1555 1.90
LINK MG MG A 601 O13 5RP A 501 1555 1555 2.26
LINK MG MG B 602 O HOH B 804 1555 1555 1.99
LINK MG MG B 602 O4 5RP B 502 1555 1555 2.14
LINK MG MG B 602 O HOH B 809 1555 1555 1.83
LINK MG MG B 602 OE2 GLU B 33 1555 1555 2.00
LINK MG MG B 602 OD2 ASP B 62 1555 1555 2.01
LINK MG MG B 602 O13 5RP B 502 1555 1555 2.47
SITE 1 AC1 19 ALA A 9 ASP A 11 GLU A 33 ASP A 62
SITE 2 AC1 19 LYS A 64 HIS A 136 THR A 169 GLY A 171
SITE 3 AC1 19 ILE A 189 GLY A 191 ARG A 192 MG A 601
SITE 4 AC1 19 HOH A 605 HOH A 629 HOH A 632 HOH A 641
SITE 5 AC1 19 HOH A 692 HOH A 801 HOH A 804
SITE 1 AC2 19 ASP A 67 ALA B 9 ASP B 11 GLU B 33
SITE 2 AC2 19 ASP B 62 LYS B 64 HIS B 136 THR B 169
SITE 3 AC2 19 GLY B 171 GLY B 191 ARG B 192 MG B 602
SITE 4 AC2 19 HOH B 611 HOH B 616 HOH B 625 HOH B 633
SITE 5 AC2 19 HOH B 698 HOH B 804 HOH B 809
SITE 1 AC3 5 GLU A 33 ASP A 62 5RP A 501 HOH A 801
SITE 2 AC3 5 HOH A 804
SITE 1 AC4 5 GLU B 33 ASP B 62 5RP B 502 HOH B 804
SITE 2 AC4 5 HOH B 809
CRYST1 123.814 41.471 91.184 90.00 96.65 90.00 C 1 2 1 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 0.008077 0.000000 0.000941 0.00000
SCALE2 0.000000 0.024113 0.000000 0.00000
SCALE3 0.000000 0.000000 0.011041 0.00000
(ATOM LINES ARE NOT SHOWN.)
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