HEADER TRANSFERASE 23-OCT-03 1R8A
TITLE CRYSTAL STRUCTURES OF AN ARCHAEAL CLASS I CCA-ADDING ENZYME AND ITS
TITLE 2 NUCLEOTIDE COMPLEXES
COMPND MOL_ID: 1;
COMPND 2 MOLECULE: TRNA NUCLEOTIDYLTRANSFERASE;
COMPND 3 CHAIN: A;
COMPND 4 SYNONYM: TRNA ADENYLYLTRANSFERASE, TRNA CCA-PYROPHOSPHORYLASE, CCA-
COMPND 5 ADDING ENZYME;
COMPND 6 EC: 2.7.7.25;
COMPND 7 ENGINEERED: YES
SOURCE MOL_ID: 1;
SOURCE 2 ORGANISM_SCIENTIFIC: ARCHAEOGLOBUS FULGIDUS;
SOURCE 3 ORGANISM_TAXID: 2234;
SOURCE 4 GENE: CCA, AF2156;
SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI;
SOURCE 6 EXPRESSION_SYSTEM_TAXID: 562
KEYWDS CCA ADDING ENZYME, NUCLEOTIDYLTRANSFERASE, TRANSFERASE
EXPDTA X-RAY DIFFRACTION
AUTHOR Y.XIONG,F.LI,J.WANG,A.M.WEINER,T.A.STEITZ
REVDAT 4 14-FEB-24 1R8A 1 REMARK LINK
REVDAT 3 13-JUL-11 1R8A 1 VERSN
REVDAT 2 24-FEB-09 1R8A 1 VERSN
REVDAT 1 16-DEC-03 1R8A 0
JRNL AUTH Y.XIONG,F.LI,J.WANG,A.M.WEINER,T.A.STEITZ
JRNL TITL CRYSTAL STRUCTURES OF AN ARCHAEAL CLASS I CCA-ADDING ENZYME
JRNL TITL 2 AND ITS NUCLEOTIDE COMPLEXES
JRNL REF MOL.CELL V. 12 1165 2003
JRNL REFN ISSN 1097-2765
JRNL PMID 14636575
JRNL DOI 10.1016/S1097-2765(03)00440-4
REMARK 2
REMARK 2 RESOLUTION. 2.10 ANGSTROMS.
REMARK 3
REMARK 3 REFINEMENT.
REMARK 3 PROGRAM : REFMAC 5.1.24
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) : 2.10
REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 38.35
REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL
REMARK 3 COMPLETENESS FOR RANGE (%) : 99.3
REMARK 3 NUMBER OF REFLECTIONS : 28329
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) : 0.189
REMARK 3 R VALUE (WORKING SET) : 0.186
REMARK 3 FREE R VALUE : 0.242
REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.100
REMARK 3 FREE R VALUE TEST SET COUNT : 1533
REMARK 3
REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN.
REMARK 3 TOTAL NUMBER OF BINS USED : 10
REMARK 3 BIN RESOLUTION RANGE HIGH (A) : 2.10
REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.21
REMARK 3 REFLECTION IN BIN (WORKING SET) : 4121
REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : NULL
REMARK 3 BIN R VALUE (WORKING SET) : 0.2280
REMARK 3 BIN FREE R VALUE SET COUNT : 248
REMARK 3 BIN FREE R VALUE : 0.2740
REMARK 3
REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT.
REMARK 3 PROTEIN ATOMS : 3630
REMARK 3 NUCLEIC ACID ATOMS : 0
REMARK 3 HETEROGEN ATOMS : 3
REMARK 3 SOLVENT ATOMS : 328
REMARK 3
REMARK 3 B VALUES.
REMARK 3 B VALUE TYPE : LIKELY RESIDUAL
REMARK 3 FROM WILSON PLOT (A**2) : NULL
REMARK 3 MEAN B VALUE (OVERALL, A**2) : 25.70
REMARK 3 OVERALL ANISOTROPIC B VALUE.
REMARK 3 B11 (A**2) : 0.61000
REMARK 3 B22 (A**2) : 1.66000
REMARK 3 B33 (A**2) : -2.10000
REMARK 3 B12 (A**2) : 0.00000
REMARK 3 B13 (A**2) : 0.60000
REMARK 3 B23 (A**2) : 0.00000
REMARK 3
REMARK 3 ESTIMATED OVERALL COORDINATE ERROR.
REMARK 3 ESU BASED ON R VALUE (A): 0.225
REMARK 3 ESU BASED ON FREE R VALUE (A): 0.194
REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.150
REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 5.733
REMARK 3
REMARK 3 CORRELATION COEFFICIENTS.
REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.945
REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.915
REMARK 3
REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT
REMARK 3 BOND LENGTHS REFINED ATOMS (A): 3713 ; 0.018 ; 0.021
REMARK 3 BOND LENGTHS OTHERS (A): 3431 ; 0.002 ; 0.020
REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 4988 ; 1.468 ; 1.961
REMARK 3 BOND ANGLES OTHERS (DEGREES): 7961 ; 0.837 ; 3.000
REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 436 ; 6.477 ; 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): 518 ; 0.089 ; 0.200
REMARK 3 GENERAL PLANES REFINED ATOMS (A): 4094 ; 0.006 ; 0.020
REMARK 3 GENERAL PLANES OTHERS (A): 840 ; 0.004 ; 0.020
REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): 801 ; 0.217 ; 0.200
REMARK 3 NON-BONDED CONTACTS OTHERS (A): 3917 ; 0.235 ; 0.200
REMARK 3 NON-BONDED TORSION REFINED ATOMS (A): NULL ; NULL ; NULL
REMARK 3 NON-BONDED TORSION OTHERS (A): 2358 ; 0.088 ; 0.200
REMARK 3 H-BOND (X...Y) REFINED ATOMS (A): 217 ; 0.220 ; 0.200
REMARK 3 H-BOND (X...Y) OTHERS (A): NULL ; NULL ; NULL
REMARK 3 POTENTIAL METAL-ION REFINED ATOMS (A): 3 ; 0.355 ; 0.200
REMARK 3 POTENTIAL METAL-ION OTHERS (A): NULL ; NULL ; NULL
REMARK 3 SYMMETRY VDW REFINED ATOMS (A): 25 ; 0.204 ; 0.200
REMARK 3 SYMMETRY VDW OTHERS (A): 160 ; 0.278 ; 0.200
REMARK 3 SYMMETRY H-BOND REFINED ATOMS (A): 31 ; 0.203 ; 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): 2176 ; 1.579 ; 2.500
REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL
REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 3513 ; 2.646 ; 4.000
REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL
REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 1537 ; 3.989 ; 5.000
REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL
REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 1475 ; 6.094 ; 8.000
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 : 4
REMARK 3
REMARK 3 TLS GROUP : 1
REMARK 3 NUMBER OF COMPONENTS GROUP : 1
REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI
REMARK 3 RESIDUE RANGE : A 17 A 124
REMARK 3 ORIGIN FOR THE GROUP (A): 14.3330 12.5031 46.0556
REMARK 3 T TENSOR
REMARK 3 T11: 0.6111 T22: 0.3381
REMARK 3 T33: 0.3451 T12: 0.3159
REMARK 3 T13: -0.0587 T23: 0.0303
REMARK 3 L TENSOR
REMARK 3 L11: 1.3460 L22: 7.3954
REMARK 3 L33: 20.8138 L12: 0.4795
REMARK 3 L13: 0.4258 L23: -2.2510
REMARK 3 S TENSOR
REMARK 3 S11: -0.6297 S12: -0.2490 S13: -0.1864
REMARK 3 S21: 1.5551 S22: 0.1922 S23: -0.9978
REMARK 3 S31: -0.4601 S32: 0.3733 S33: 0.4375
REMARK 3
REMARK 3 TLS GROUP : 2
REMARK 3 NUMBER OF COMPONENTS GROUP : 2
REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI
REMARK 3 RESIDUE RANGE : A 125 A 258
REMARK 3 RESIDUE RANGE : A 1 A 16
REMARK 3 ORIGIN FOR THE GROUP (A): 10.7788 13.2919 20.8457
REMARK 3 T TENSOR
REMARK 3 T11: 0.0763 T22: 0.2897
REMARK 3 T33: 0.2060 T12: 0.1172
REMARK 3 T13: 0.0275 T23: 0.0362
REMARK 3 L TENSOR
REMARK 3 L11: 2.1541 L22: 3.6355
REMARK 3 L33: 3.8495 L12: -1.3907
REMARK 3 L13: -0.4324 L23: 0.5186
REMARK 3 S TENSOR
REMARK 3 S11: -0.2057 S12: -0.2550 S13: -0.2324
REMARK 3 S21: 0.2784 S22: 0.1477 S23: 0.4456
REMARK 3 S31: 0.0898 S32: -0.6712 S33: 0.0581
REMARK 3
REMARK 3 TLS GROUP : 3
REMARK 3 NUMBER OF COMPONENTS GROUP : 1
REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI
REMARK 3 RESIDUE RANGE : A 338 A 382
REMARK 3 ORIGIN FOR THE GROUP (A): 62.5489 1.1468 -0.0555
REMARK 3 T TENSOR
REMARK 3 T11: 0.2329 T22: 0.1915
REMARK 3 T33: 0.2132 T12: -0.0153
REMARK 3 T13: -0.0459 T23: -0.0231
REMARK 3 L TENSOR
REMARK 3 L11: 2.2195 L22: 3.4255
REMARK 3 L33: 1.3759 L12: 2.3494
REMARK 3 L13: -0.8613 L23: -1.5431
REMARK 3 S TENSOR
REMARK 3 S11: 0.0817 S12: -0.2395 S13: 0.0790
REMARK 3 S21: 0.3793 S22: -0.0549 S23: -0.1937
REMARK 3 S31: -0.2189 S32: 0.4373 S33: -0.0267
REMARK 3
REMARK 3 TLS GROUP : 4
REMARK 3 NUMBER OF COMPONENTS GROUP : 2
REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI
REMARK 3 RESIDUE RANGE : A 259 A 337
REMARK 3 RESIDUE RANGE : A 383 A 437
REMARK 3 ORIGIN FOR THE GROUP (A): 35.2637 -7.8565 17.3934
REMARK 3 T TENSOR
REMARK 3 T11: 0.2157 T22: 0.0918
REMARK 3 T33: 0.1723 T12: 0.0645
REMARK 3 T13: 0.0100 T23: 0.0070
REMARK 3 L TENSOR
REMARK 3 L11: 2.4170 L22: 1.1742
REMARK 3 L33: 3.8062 L12: -0.8416
REMARK 3 L13: -0.1153 L23: 0.0623
REMARK 3 S TENSOR
REMARK 3 S11: -0.2212 S12: -0.3540 S13: -0.0227
REMARK 3 S21: 0.1148 S22: 0.2333 S23: 0.0226
REMARK 3 S31: 0.3427 S32: -0.1309 S33: -0.0121
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: HYDROGENS HAVE BEEN ADDED IN THE RIDING
REMARK 3 POSITIONS
REMARK 4
REMARK 4 1R8A COMPLIES WITH FORMAT V. 3.30, 13-JUL-11
REMARK 100
REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 24-OCT-03.
REMARK 100 THE DEPOSITION ID IS D_1000020560.
REMARK 200
REMARK 200 EXPERIMENTAL DETAILS
REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION
REMARK 200 DATE OF DATA COLLECTION : NULL
REMARK 200 TEMPERATURE (KELVIN) : 100
REMARK 200 PH : 6.4
REMARK 200 NUMBER OF CRYSTALS USED : 1
REMARK 200
REMARK 200 SYNCHROTRON (Y/N) : Y
REMARK 200 RADIATION SOURCE : NSLS
REMARK 200 BEAMLINE : X26C
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 : ADSC QUANTUM 4
REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000
REMARK 200 DATA SCALING SOFTWARE : SCALEPACK
REMARK 200
REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 29906
REMARK 200 RESOLUTION RANGE HIGH (A) : 2.100
REMARK 200 RESOLUTION RANGE LOW (A) : 40.000
REMARK 200 REJECTION CRITERIA (SIGMA(I)) : -3.000
REMARK 200
REMARK 200 OVERALL.
REMARK 200 COMPLETENESS FOR RANGE (%) : NULL
REMARK 200 DATA REDUNDANCY : 3.600
REMARK 200 R MERGE (I) : NULL
REMARK 200 R SYM (I) : 0.08100
REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 16.0000
REMARK 200
REMARK 200 IN THE HIGHEST RESOLUTION SHELL.
REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.10
REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.18
REMARK 200 COMPLETENESS FOR SHELL (%) : 99.9
REMARK 200 DATA REDUNDANCY IN SHELL : NULL
REMARK 200 R MERGE FOR SHELL (I) : NULL
REMARK 200 R SYM FOR SHELL (I) : NULL
REMARK 200 <I/SIGMA(I)> FOR SHELL : NULL
REMARK 200
REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH
REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT
REMARK 200 SOFTWARE USED: AMORE
REMARK 200 STARTING MODEL: NULL
REMARK 200
REMARK 200 REMARK: NULL
REMARK 280
REMARK 280 CRYSTAL
REMARK 280 SOLVENT CONTENT, VS (%): 51.43
REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.53
REMARK 280
REMARK 280 CRYSTALLIZATION CONDITIONS: CALCIUM CHLORIDE, ETHANOL, TRIS,
REMARK 280 MAGNESIUM CHLORIDE, SODIUM CHLORIDE, PH 6.4, VAPOR DIFFUSION,
REMARK 280 HANGING DROP, TEMPERATURE 293K
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 43.22650
REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 39.36300
REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 0.00000
REMARK 290 SMTRY1 4 -1.000000 0.000000 0.000000 43.22650
REMARK 290 SMTRY2 4 0.000000 1.000000 0.000000 39.36300
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: DIMERIC
REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC
REMARK 350 SOFTWARE USED: PISA,PQS
REMARK 350 TOTAL BURIED SURFACE AREA: 5490 ANGSTROM**2
REMARK 350 SURFACE AREA OF THE COMPLEX: 43680 ANGSTROM**2
REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -30.0 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 86.45300
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 883 LIES ON A SPECIAL POSITION.
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 804 O HOH A 840 2.00
REMARK 500 O HOH A 648 O HOH A 785 2.06
REMARK 500 O HOH A 606 O HOH A 747 2.08
REMARK 500 O HOH A 618 O HOH A 831 2.11
REMARK 500 O ARG A 268 O HOH A 765 2.19
REMARK 500 O HOH A 831 O HOH A 920 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 MET A 314 SD MET A 314 CE -0.419
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 110 CB - CG - OD2 ANGL. DEV. = 5.5 DEGREES
REMARK 500 ASP A 202 CB - CG - OD2 ANGL. DEV. = 5.7 DEGREES
REMARK 500 ASP A 233 CB - CG - OD2 ANGL. DEV. = 6.2 DEGREES
REMARK 500 ARG A 274 NE - CZ - NH1 ANGL. DEV. = 3.3 DEGREES
REMARK 500 ASP A 290 CB - CG - OD2 ANGL. DEV. = 5.5 DEGREES
REMARK 500 ARG A 340 NE - CZ - NH2 ANGL. DEV. = -3.6 DEGREES
REMARK 500 ARG A 373 NE - CZ - NH2 ANGL. DEV. = -3.5 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 LYS A 2 127.64 73.60
REMARK 500 SER A 57 51.50 -110.95
REMARK 500 GLU A 96 -48.73 -140.20
REMARK 500 GLU A 119 125.36 73.99
REMARK 500 PRO A 120 -160.60 -69.54
REMARK 500 ASN A 122 37.80 -147.99
REMARK 500 GLU A 261 69.22 36.85
REMARK 500 SER A 323 -166.84 -102.32
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 MN A 604 MN
REMARK 620 N RES CSSEQI ATOM
REMARK 620 1 GLU A 59 OE2
REMARK 620 2 ASP A 61 OD1 161.8
REMARK 620 3 ASP A 110 OD2 89.5 83.6
REMARK 620 4 HOH A 750 O 105.9 89.4 78.8
REMARK 620 N 1 2 3
REMARK 620
REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL
REMARK 620 MN A 603 MN
REMARK 620 N RES CSSEQI ATOM
REMARK 620 1 HIS A 133 NE2
REMARK 620 2 ASP A 218 OD2 103.4
REMARK 620 N 1
REMARK 620
REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL
REMARK 620 NA A 605 NA
REMARK 620 N RES CSSEQI ATOM
REMARK 620 1 LYS A 205 O
REMARK 620 2 SER A 391 OG 98.3
REMARK 620 3 SER A 391 O 83.1 73.2
REMARK 620 4 THR A 395 OG1 94.5 151.7 83.4
REMARK 620 5 HOH A 766 O 119.9 94.3 155.7 101.1
REMARK 620 N 1 2 3 4
REMARK 800
REMARK 800 SITE
REMARK 800 SITE_IDENTIFIER: AC1
REMARK 800 EVIDENCE_CODE: SOFTWARE
REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MN A 603
REMARK 800
REMARK 800 SITE_IDENTIFIER: AC2
REMARK 800 EVIDENCE_CODE: SOFTWARE
REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MN A 604
REMARK 800
REMARK 800 SITE_IDENTIFIER: AC3
REMARK 800 EVIDENCE_CODE: SOFTWARE
REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE NA A 605
REMARK 900
REMARK 900 RELATED ENTRIES
REMARK 900 RELATED ID: 1R89 RELATED DB: PDB
REMARK 900 SAME PROTEIN COMPLEXED WITH CTP
REMARK 900 RELATED ID: 1R8B RELATED DB: PDB
REMARK 900 SAME PROTEIN COMPLEXED WITH ATP
REMARK 900 RELATED ID: 1R8C RELATED DB: PDB
REMARK 900 SAME PROTEIN COMPLEXED WITH UTP
DBREF 1R8A A 1 437 UNP O28126 CCA_ARCFU 1 437
SEQRES 1 A 437 MET LYS VAL GLU GLU ILE LEU GLU LYS ALA LEU GLU LEU
SEQRES 2 A 437 VAL ILE PRO ASP GLU GLU GLU VAL ARG LYS GLY ARG GLU
SEQRES 3 A 437 ALA GLU GLU GLU LEU ARG ARG ARG LEU ASP GLU LEU GLY
SEQRES 4 A 437 VAL GLU TYR VAL PHE VAL GLY SER TYR ALA ARG ASN THR
SEQRES 5 A 437 TRP LEU LYS GLY SER LEU GLU ILE ASP VAL PHE LEU LEU
SEQRES 6 A 437 PHE PRO GLU GLU PHE SER LYS GLU GLU LEU ARG GLU ARG
SEQRES 7 A 437 GLY LEU GLU ILE GLY LYS ALA VAL LEU ASP SER TYR GLU
SEQRES 8 A 437 ILE ARG TYR ALA GLU HIS PRO TYR VAL HIS GLY VAL VAL
SEQRES 9 A 437 LYS GLY VAL GLU VAL ASP VAL VAL PRO CYS TYR LYS LEU
SEQRES 10 A 437 LYS GLU PRO LYS ASN ILE LYS SER ALA VAL ASP ARG THR
SEQRES 11 A 437 PRO PHE HIS HIS LYS TRP LEU GLU GLY ARG ILE LYS GLY
SEQRES 12 A 437 LYS GLU ASN GLU VAL ARG LEU LEU LYS GLY PHE LEU LYS
SEQRES 13 A 437 ALA ASN GLY ILE TYR GLY ALA GLU TYR LYS VAL ARG GLY
SEQRES 14 A 437 PHE SER GLY TYR LEU CYS GLU LEU LEU ILE VAL PHE TYR
SEQRES 15 A 437 GLY SER PHE LEU GLU THR VAL LYS ASN ALA ARG ARG TRP
SEQRES 16 A 437 THR ARG ARG THR VAL ILE ASP VAL ALA LYS GLY GLU VAL
SEQRES 17 A 437 ARG LYS GLY GLU GLU PHE PHE VAL VAL ASP PRO VAL ASP
SEQRES 18 A 437 GLU LYS ARG ASN VAL ALA ALA ASN LEU SER LEU ASP ASN
SEQRES 19 A 437 LEU ALA ARG PHE VAL HIS LEU CYS ARG GLU PHE MET GLU
SEQRES 20 A 437 ALA PRO SER LEU GLY PHE PHE LYS PRO LYS HIS PRO LEU
SEQRES 21 A 437 GLU ILE GLU PRO GLU ARG LEU ARG LYS ILE VAL GLU GLU
SEQRES 22 A 437 ARG GLY THR ALA VAL PHE ALA VAL LYS PHE ARG LYS PRO
SEQRES 23 A 437 ASP ILE VAL ASP ASP ASN LEU TYR PRO GLN LEU GLU ARG
SEQRES 24 A 437 ALA SER ARG LYS ILE PHE GLU PHE LEU GLU ARG GLU ASN
SEQRES 25 A 437 PHE MET PRO LEU ARG SER ALA PHE LYS ALA SER GLU GLU
SEQRES 26 A 437 PHE CYS TYR LEU LEU PHE GLU CYS GLN ILE LYS GLU ILE
SEQRES 27 A 437 SER ARG VAL PHE ARG ARG MET GLY PRO GLN PHE GLU ASP
SEQRES 28 A 437 GLU ARG ASN VAL LYS LYS PHE LEU SER ARG ASN ARG ALA
SEQRES 29 A 437 PHE ARG PRO PHE ILE GLU ASN GLY ARG TRP TRP ALA PHE
SEQRES 30 A 437 GLU MET ARG LYS PHE THR THR PRO GLU GLU GLY VAL ARG
SEQRES 31 A 437 SER TYR ALA SER THR HIS TRP HIS THR LEU GLY LYS ASN
SEQRES 32 A 437 VAL GLY GLU SER ILE ARG GLU TYR PHE GLU ILE ILE SER
SEQRES 33 A 437 GLY GLU LYS LEU PHE LYS GLU PRO VAL THR ALA GLU LEU
SEQRES 34 A 437 CYS GLU MET MET GLY VAL LYS ASP
HET MN A 603 1
HET MN A 604 1
HET NA A 605 1
HETNAM MN MANGANESE (II) ION
HETNAM NA SODIUM ION
FORMUL 2 MN 2(MN 2+)
FORMUL 4 NA NA 1+
FORMUL 5 HOH *328(H2 O)
HELIX 1 1 LYS A 2 ILE A 15 1 14
HELIX 2 2 ASP A 17 GLY A 39 1 23
HELIX 3 3 GLY A 46 ARG A 50 1 5
HELIX 4 4 GLU A 73 LEU A 87 1 15
HELIX 5 5 ARG A 129 GLU A 138 1 10
HELIX 6 6 LYS A 144 ASN A 158 1 15
HELIX 7 7 SER A 171 GLY A 183 1 13
HELIX 8 8 SER A 184 ARG A 193 1 10
HELIX 9 9 ALA A 204 GLY A 206 5 3
HELIX 10 10 SER A 231 ALA A 248 1 18
HELIX 11 11 SER A 250 LYS A 255 5 6
HELIX 12 12 GLU A 263 GLY A 275 1 13
HELIX 13 13 VAL A 289 GLU A 311 1 23
HELIX 14 14 ASP A 351 ARG A 361 1 11
HELIX 15 15 THR A 384 HIS A 396 1 13
HELIX 16 16 TRP A 397 LEU A 400 5 4
HELIX 17 17 GLY A 401 TYR A 411 1 11
HELIX 18 18 GLY A 417 PHE A 421 1 5
HELIX 19 19 VAL A 425 GLY A 434 1 10
SHEET 1 A 5 TYR A 42 VAL A 45 0
SHEET 2 A 5 ILE A 60 PHE A 66 -1 O PHE A 63 N VAL A 43
SHEET 3 A 5 GLU A 108 TYR A 115 1 O ASP A 110 N VAL A 62
SHEET 4 A 5 PRO A 98 VAL A 103 -1 N VAL A 100 O VAL A 111
SHEET 5 A 5 ILE A 92 TYR A 94 -1 N ARG A 93 O TYR A 99
SHEET 1 B 3 GLU A 207 LYS A 210 0
SHEET 2 B 3 THR A 199 ASP A 202 -1 N VAL A 200 O ARG A 209
SHEET 3 B 3 PHE A 215 VAL A 217 1 O VAL A 217 N ILE A 201
SHEET 1 C 4 PRO A 315 ALA A 322 0
SHEET 2 C 4 PHE A 326 CYS A 333 -1 O LEU A 330 N ALA A 319
SHEET 3 C 4 ALA A 277 ARG A 284 -1 N VAL A 281 O LEU A 329
SHEET 4 C 4 PHE A 412 SER A 416 -1 O ILE A 415 N ALA A 280
SHEET 1 D 3 VAL A 341 GLN A 348 0
SHEET 2 D 3 ARG A 373 MET A 379 -1 O ALA A 376 N ARG A 344
SHEET 3 D 3 PHE A 368 GLU A 370 -1 N GLU A 370 O ARG A 373
LINK OE2 GLU A 59 MN MN A 604 1555 1555 2.76
LINK OD1 ASP A 61 MN MN A 604 1555 1555 2.20
LINK OD2 ASP A 110 MN MN A 604 1555 1555 1.71
LINK NE2 HIS A 133 MN MN A 603 1555 1555 2.12
LINK O LYS A 205 NA NA A 605 3545 1555 2.39
LINK OD2 ASP A 218 MN MN A 603 1555 1555 1.75
LINK OG SER A 391 NA NA A 605 1555 1555 2.57
LINK O SER A 391 NA NA A 605 1555 1555 2.76
LINK OG1 THR A 395 NA NA A 605 1555 1555 2.27
LINK MN MN A 604 O HOH A 750 1555 1555 2.60
LINK NA NA A 605 O HOH A 766 1555 1555 1.81
SITE 1 AC1 3 ARG A 129 HIS A 133 ASP A 218
SITE 1 AC2 4 GLU A 59 ASP A 61 ASP A 110 HOH A 750
SITE 1 AC3 4 LYS A 205 SER A 391 THR A 395 HOH A 766
CRYST1 86.453 78.726 77.396 90.00 98.03 90.00 C 1 2 1 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 0.011567 0.000000 0.001632 0.00000
SCALE2 0.000000 0.012702 0.000000 0.00000
SCALE3 0.000000 0.000000 0.013049 0.00000
(ATOM LINES ARE NOT SHOWN.)
END