HEADER OXIDOREDUCTASE 28-JUN-10 3NPE
TITLE STRUCTURE OF VP14 IN COMPLEX WITH OXYGEN
COMPND MOL_ID: 1;
COMPND 2 MOLECULE: 9-CIS-EPOXYCAROTENOID DIOXYGENASE 1, CHLOROPLASTIC;
COMPND 3 CHAIN: A;
COMPND 4 SYNONYM: PROTEIN VIVIPAROUS14, VP-14;
COMPND 5 EC: 1.13.11.51;
COMPND 6 ENGINEERED: YES
SOURCE MOL_ID: 1;
SOURCE 2 ORGANISM_SCIENTIFIC: ZEA MAYS;
SOURCE 3 ORGANISM_COMMON: MAIZE;
SOURCE 4 ORGANISM_TAXID: 4577;
SOURCE 5 GENE: VP14;
SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI;
SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562;
SOURCE 8 EXPRESSION_SYSTEM_STRAIN: M15;
SOURCE 9 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID;
SOURCE 10 EXPRESSION_SYSTEM_PLASMID: PMAL C2X HV
KEYWDS DIOXYGENASE, SEVEN BLADE BETA PROPELLER, ABSCISIC ACID, NON HEME
KEYWDS 2 IRON, OXIDOREDUCTASE
EXPDTA X-RAY DIFFRACTION
AUTHOR S.A.MESSING,S.B.GABELLI,L.M.AMZEL
REVDAT 4 27-DEC-23 3NPE 1 REMARK LINK
REVDAT 3 08-NOV-17 3NPE 1 REMARK
REVDAT 2 17-NOV-10 3NPE 1 JRNL
REVDAT 1 10-NOV-10 3NPE 0
JRNL AUTH S.A.MESSING,S.B.GABELLI,I.ECHEVERRIA,J.T.VOGEL,J.C.GUAN,
JRNL AUTH 2 B.C.TAN,H.J.KLEE,D.R.MCCARTY,L.M.AMZEL
JRNL TITL STRUCTURAL INSIGHTS INTO MAIZE VIVIPAROUS14, A KEY ENZYME IN
JRNL TITL 2 THE BIOSYNTHESIS OF THE PHYTOHORMONE ABSCISIC ACID.
JRNL REF PLANT CELL V. 22 2970 2010
JRNL REFN ISSN 1040-4651
JRNL PMID 20884803
JRNL DOI 10.1105/TPC.110.074815
REMARK 2
REMARK 2 RESOLUTION. 3.20 ANGSTROMS.
REMARK 3
REMARK 3 REFINEMENT.
REMARK 3 PROGRAM : REFMAC
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) : 3.20
REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 47.30
REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL
REMARK 3 COMPLETENESS FOR RANGE (%) : 99.7
REMARK 3 NUMBER OF REFLECTIONS : 18636
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) : 0.242
REMARK 3 R VALUE (WORKING SET) : 0.241
REMARK 3 FREE R VALUE : 0.272
REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.200
REMARK 3 FREE R VALUE TEST SET COUNT : 1016
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) : 3.20
REMARK 3 BIN RESOLUTION RANGE LOW (A) : 3.28
REMARK 3 REFLECTION IN BIN (WORKING SET) : 1318
REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 99.93
REMARK 3 BIN R VALUE (WORKING SET) : 0.3200
REMARK 3 BIN FREE R VALUE SET COUNT : 88
REMARK 3 BIN FREE R VALUE : 0.3490
REMARK 3
REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT.
REMARK 3 PROTEIN ATOMS : 4010
REMARK 3 NUCLEIC ACID ATOMS : 0
REMARK 3 HETEROGEN ATOMS : 22
REMARK 3 SOLVENT ATOMS : 10
REMARK 3
REMARK 3 B VALUES.
REMARK 3 FROM WILSON PLOT (A**2) : NULL
REMARK 3 MEAN B VALUE (OVERALL, A**2) : 85.29
REMARK 3 OVERALL ANISOTROPIC B VALUE.
REMARK 3 B11 (A**2) : 1.45000
REMARK 3 B22 (A**2) : 1.45000
REMARK 3 B33 (A**2) : -2.18000
REMARK 3 B12 (A**2) : 0.73000
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): 1.004
REMARK 3 ESU BASED ON FREE R VALUE (A): 0.412
REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.354
REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 46.123
REMARK 3
REMARK 3 CORRELATION COEFFICIENTS.
REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.913
REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.886
REMARK 3
REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT
REMARK 3 BOND LENGTHS REFINED ATOMS (A): 4138 ; 0.013 ; 0.022
REMARK 3 BOND LENGTHS OTHERS (A): NULL ; NULL ; NULL
REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 5618 ; 1.466 ; 1.960
REMARK 3 BOND ANGLES OTHERS (DEGREES): NULL ; NULL ; NULL
REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 521 ; 8.574 ; 5.000
REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 198 ;36.003 ;23.283
REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 614 ;21.840 ;15.000
REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 35 ;19.536 ;15.000
REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 607 ; 0.105 ; 0.200
REMARK 3 GENERAL PLANES REFINED ATOMS (A): 3253 ; 0.004 ; 0.020
REMARK 3 GENERAL PLANES OTHERS (A): NULL ; NULL ; NULL
REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): 1903 ; 0.236 ; 0.200
REMARK 3 NON-BONDED CONTACTS OTHERS (A): NULL ; NULL ; NULL
REMARK 3 NON-BONDED TORSION REFINED ATOMS (A): 2719 ; 0.319 ; 0.200
REMARK 3 NON-BONDED TORSION OTHERS (A): NULL ; NULL ; NULL
REMARK 3 H-BOND (X...Y) REFINED ATOMS (A): 166 ; 0.147 ; 0.200
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): 32 ; 0.221 ; 0.200
REMARK 3 SYMMETRY VDW OTHERS (A): NULL ; NULL ; NULL
REMARK 3 SYMMETRY H-BOND REFINED ATOMS (A): 1 ; 0.117 ; 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): 2647 ; 0.411 ; 1.500
REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL
REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 4167 ; 0.671 ; 2.000
REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL
REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 1639 ; 0.937 ; 3.000
REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL
REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 1451 ; 1.505 ; 4.500
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 : 3
REMARK 3
REMARK 3 TLS GROUP : 1
REMARK 3 NUMBER OF COMPONENTS GROUP : 2
REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI
REMARK 3 RESIDUE RANGE : A 83 A 130
REMARK 3 RESIDUE RANGE : A 196 A 248
REMARK 3 ORIGIN FOR THE GROUP (A): 6.2310 78.0400 74.1890
REMARK 3 T TENSOR
REMARK 3 T11: 0.1584 T22: 0.1454
REMARK 3 T33: -0.1090 T12: -0.0037
REMARK 3 T13: 0.2109 T23: -0.0944
REMARK 3 L TENSOR
REMARK 3 L11: 0.6645 L22: 5.8833
REMARK 3 L33: 1.0869 L12: -0.2026
REMARK 3 L13: -0.2339 L23: -1.8172
REMARK 3 S TENSOR
REMARK 3 S11: -0.1031 S12: 0.7239 S13: 0.0206
REMARK 3 S21: -0.7180 S22: -0.2789 S23: -0.0980
REMARK 3 S31: -0.2189 S32: 0.2612 S33: 0.3820
REMARK 3
REMARK 3 TLS GROUP : 2
REMARK 3 NUMBER OF COMPONENTS GROUP : 6
REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI
REMARK 3 RESIDUE RANGE : A 131 A 195
REMARK 3 RESIDUE RANGE : A 249 A 431
REMARK 3 RESIDUE RANGE : A 448 A 535
REMARK 3 RESIDUE RANGE : A 545 A 605
REMARK 3 RESIDUE RANGE : X 1 X 2
REMARK 3 RESIDUE RANGE : NULL 2946 NULL 2948
REMARK 3 ORIGIN FOR THE GROUP (A): -0.1200 53.7160 88.3050
REMARK 3 T TENSOR
REMARK 3 T11: -0.1753 T22: -0.0805
REMARK 3 T33: -0.0729 T12: -0.0205
REMARK 3 T13: 0.4727 T23: -0.2926
REMARK 3 L TENSOR
REMARK 3 L11: 2.6331 L22: 3.1388
REMARK 3 L33: 3.3740 L12: -0.3954
REMARK 3 L13: -0.7038 L23: -0.6536
REMARK 3 S TENSOR
REMARK 3 S11: -0.3339 S12: 0.4275 S13: -0.4439
REMARK 3 S21: -0.4204 S22: -0.1294 S23: 0.1553
REMARK 3 S31: 0.0542 S32: -0.1320 S33: 0.4633
REMARK 3
REMARK 3 TLS GROUP : 3
REMARK 3 NUMBER OF COMPONENTS GROUP : 2
REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI
REMARK 3 RESIDUE RANGE : A 432 A 447
REMARK 3 RESIDUE RANGE : A 536 A 544
REMARK 3 ORIGIN FOR THE GROUP (A): 4.4760 56.8110 97.3080
REMARK 3 T TENSOR
REMARK 3 T11: 0.3432 T22: 0.6509
REMARK 3 T33: 0.3220 T12: 0.3048
REMARK 3 T13: 0.2485 T23: 0.2593
REMARK 3 L TENSOR
REMARK 3 L11: 8.8580 L22: 1.4370
REMARK 3 L33: 9.8745 L12: -2.9202
REMARK 3 L13: 0.1127 L23: -2.2013
REMARK 3 S TENSOR
REMARK 3 S11: -0.1494 S12: -1.1902 S13: 0.9169
REMARK 3 S21: -2.6883 S22: -1.4132 S23: 0.3380
REMARK 3 S31: -2.0875 S32: -0.3318 S33: 1.5626
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 3NPE COMPLIES WITH FORMAT V. 3.30, 13-JUL-11
REMARK 100
REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 29-JUN-10.
REMARK 100 THE DEPOSITION ID IS D_1000060113.
REMARK 200
REMARK 200 EXPERIMENTAL DETAILS
REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION
REMARK 200 DATE OF DATA COLLECTION : 13-DEC-07
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 : 31-ID
REMARK 200 X-RAY GENERATOR MODEL : NULL
REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M
REMARK 200 WAVELENGTH OR RANGE (A) : 0.97989
REMARK 200 MONOCHROMATOR : NULL
REMARK 200 OPTICS : NULL
REMARK 200
REMARK 200 DETECTOR TYPE : CCD
REMARK 200 DETECTOR MANUFACTURER : MAR CCD 165 MM
REMARK 200 INTENSITY-INTEGRATION SOFTWARE : DENZO
REMARK 200 DATA SCALING SOFTWARE : SCALEPACK
REMARK 200
REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 23752
REMARK 200 RESOLUTION RANGE HIGH (A) : 3.000
REMARK 200 RESOLUTION RANGE LOW (A) : 50.000
REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL
REMARK 200
REMARK 200 OVERALL.
REMARK 200 COMPLETENESS FOR RANGE (%) : 99.9
REMARK 200 DATA REDUNDANCY : 18.50
REMARK 200 R MERGE (I) : 0.07500
REMARK 200 R SYM (I) : NULL
REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 6.7000
REMARK 200
REMARK 200 IN THE HIGHEST RESOLUTION SHELL.
REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 3.00
REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 3.11
REMARK 200 COMPLETENESS FOR SHELL (%) : 99.7
REMARK 200 DATA REDUNDANCY IN SHELL : 10.30
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: SOLVE 2.03, RESOLVE 2.03
REMARK 200 STARTING MODEL: NULL
REMARK 200
REMARK 200 REMARK: NULL
REMARK 280
REMARK 280 CRYSTAL
REMARK 280 SOLVENT CONTENT, VS (%): 71.64
REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 4.93
REMARK 280
REMARK 280 CRYSTALLIZATION CONDITIONS: PEG 4000, LI SULFATE, DIOXANE, 1,6
REMARK 280 HEXANDIOL, PH 7.5, HANGING DROP, TEMPERATURE 298K
REMARK 290
REMARK 290 CRYSTALLOGRAPHIC SYMMETRY
REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 63 2 2
REMARK 290
REMARK 290 SYMOP SYMMETRY
REMARK 290 NNNMMM OPERATOR
REMARK 290 1555 X,Y,Z
REMARK 290 2555 -Y,X-Y,Z
REMARK 290 3555 -X+Y,-X,Z
REMARK 290 4555 -X,-Y,Z+1/2
REMARK 290 5555 Y,-X+Y,Z+1/2
REMARK 290 6555 X-Y,X,Z+1/2
REMARK 290 7555 Y,X,-Z
REMARK 290 8555 X-Y,-Y,-Z
REMARK 290 9555 -X,-X+Y,-Z
REMARK 290 10555 -Y,-X,-Z+1/2
REMARK 290 11555 -X+Y,Y,-Z+1/2
REMARK 290 12555 X,X-Y,-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 -0.500000 -0.866025 0.000000 0.00000
REMARK 290 SMTRY2 2 0.866025 -0.500000 0.000000 0.00000
REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 0.00000
REMARK 290 SMTRY1 3 -0.500000 0.866025 0.000000 0.00000
REMARK 290 SMTRY2 3 -0.866025 -0.500000 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 75.40800
REMARK 290 SMTRY1 5 0.500000 0.866025 0.000000 0.00000
REMARK 290 SMTRY2 5 -0.866025 0.500000 0.000000 0.00000
REMARK 290 SMTRY3 5 0.000000 0.000000 1.000000 75.40800
REMARK 290 SMTRY1 6 0.500000 -0.866025 0.000000 0.00000
REMARK 290 SMTRY2 6 0.866025 0.500000 0.000000 0.00000
REMARK 290 SMTRY3 6 0.000000 0.000000 1.000000 75.40800
REMARK 290 SMTRY1 7 -0.500000 0.866025 0.000000 0.00000
REMARK 290 SMTRY2 7 0.866025 0.500000 0.000000 0.00000
REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 0.00000
REMARK 290 SMTRY1 8 1.000000 0.000000 0.000000 0.00000
REMARK 290 SMTRY2 8 0.000000 -1.000000 0.000000 0.00000
REMARK 290 SMTRY3 8 0.000000 0.000000 -1.000000 0.00000
REMARK 290 SMTRY1 9 -0.500000 -0.866025 0.000000 0.00000
REMARK 290 SMTRY2 9 -0.866025 0.500000 0.000000 0.00000
REMARK 290 SMTRY3 9 0.000000 0.000000 -1.000000 0.00000
REMARK 290 SMTRY1 10 0.500000 -0.866025 0.000000 0.00000
REMARK 290 SMTRY2 10 -0.866025 -0.500000 0.000000 0.00000
REMARK 290 SMTRY3 10 0.000000 0.000000 -1.000000 75.40800
REMARK 290 SMTRY1 11 -1.000000 0.000000 0.000000 0.00000
REMARK 290 SMTRY2 11 0.000000 1.000000 0.000000 0.00000
REMARK 290 SMTRY3 11 0.000000 0.000000 -1.000000 75.40800
REMARK 290 SMTRY1 12 0.500000 0.866025 0.000000 0.00000
REMARK 290 SMTRY2 12 0.866025 -0.500000 0.000000 0.00000
REMARK 290 SMTRY3 12 0.000000 0.000000 -1.000000 75.40800
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 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 LYS A 76
REMARK 465 ALA A 77
REMARK 465 GLU A 78
REMARK 465 GLY A 79
REMARK 465 GLY A 80
REMARK 465 LYS A 81
REMARK 465 LYS A 82
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 PRO A 140 CD PRO A 140 N 0.092
REMARK 500 VAL A 579 CB VAL A 579 CG1 0.184
REMARK 500 VAL A 579 CB VAL A 579 CG2 0.243
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 PRO A 500 C - N - CA ANGL. DEV. = 10.5 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 LEU A 84 -108.20 -80.13
REMARK 500 ASN A 85 -150.30 -138.09
REMARK 500 PHE A 102 -73.54 -115.89
REMARK 500 VAL A 106 -60.40 -94.62
REMARK 500 ALA A 124 152.71 -48.89
REMARK 500 ASN A 159 72.48 -153.78
REMARK 500 ALA A 166 138.99 -35.20
REMARK 500 HIS A 168 125.03 -172.39
REMARK 500 GLU A 196 76.70 -69.08
REMARK 500 ALA A 198 -35.51 -32.33
REMARK 500 VAL A 210 -34.57 -134.64
REMARK 500 PHE A 287 85.56 -66.22
REMARK 500 HIS A 298 61.25 -115.52
REMARK 500 ILE A 316 -68.52 -108.22
REMARK 500 ARG A 318 -58.96 -26.67
REMARK 500 HIS A 393 49.91 -97.93
REMARK 500 SER A 437 -147.70 -105.55
REMARK 500 SER A 442 7.22 -165.07
REMARK 500 ASP A 443 -163.99 -116.47
REMARK 500 ARG A 445 76.63 70.58
REMARK 500 SER A 471 -78.68 -72.25
REMARK 500 GLU A 477 -155.37 -96.71
REMARK 500 VAL A 478 136.43 -33.97
REMARK 500 ASN A 482 106.80 -47.57
REMARK 500 ARG A 483 -37.83 -36.13
REMARK 500 TRP A 501 -94.21 -7.16
REMARK 500 MET A 536 99.98 -61.87
REMARK 500 ALA A 539 48.89 100.03
REMARK 500 ALA A 540 -83.76 -105.38
REMARK 500 ALA A 541 -80.60 -79.38
REMARK 500 HIS A 542 -75.59 -138.82
REMARK 500 GLU A 546 -36.93 -37.10
REMARK 500 THR A 562 -155.28 -88.77
REMARK 500 SER A 583 -146.29 -85.13
REMARK 500 PHE A 589 -127.00 -111.00
REMARK 500 GLN A 602 -66.06 -25.84
REMARK 500 ALA A 603 105.52 37.17
REMARK 500
REMARK 500 REMARK: NULL
REMARK 500
REMARK 500 GEOMETRY AND STEREOCHEMISTRY
REMARK 500 SUBTOPIC: NON-CIS, NON-TRANS
REMARK 500
REMARK 500 THE FOLLOWING PEPTIDE BONDS DEVIATE SIGNIFICANTLY FROM BOTH
REMARK 500 CIS AND TRANS CONFORMATION. CIS BONDS, IF ANY, ARE LISTED
REMARK 500 ON CISPEP RECORDS. TRANS IS DEFINED AS 180 +/- 30 AND
REMARK 500 CIS IS DEFINED AS 0 +/- 30 DEGREES.
REMARK 500 MODEL OMEGA
REMARK 500 GLU A 499 PRO A 500 111.57
REMARK 500 PRO A 500 TRP A 501 -148.74
REMARK 500 ASP A 537 PRO A 538 -132.14
REMARK 500 HIS A 542 PRO A 543 149.69
REMARK 500 GLU A 558 ARG A 559 -146.30
REMARK 500 ALA A 560 GLY A 561 149.58
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 FE2 A 605 FE
REMARK 620 N RES CSSEQI ATOM
REMARK 620 1 OXY A 1 O2
REMARK 620 2 OH A 2 O 73.8
REMARK 620 3 HIS A 298 NE2 151.5 78.0
REMARK 620 4 HIS A 347 NE2 91.7 88.9 92.0
REMARK 620 5 HIS A 412 NE2 106.5 176.4 101.3 94.6
REMARK 620 6 HIS A 590 NE2 76.9 80.3 94.4 166.1 96.2
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 FE2 A 605
REMARK 800
REMARK 800 SITE_IDENTIFIER: AC2
REMARK 800 EVIDENCE_CODE: SOFTWARE
REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE OXY A 1
REMARK 800
REMARK 800 SITE_IDENTIFIER: AC3
REMARK 800 EVIDENCE_CODE: SOFTWARE
REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE OH A 2
REMARK 800
REMARK 800 SITE_IDENTIFIER: AC4
REMARK 800 EVIDENCE_CODE: SOFTWARE
REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE DIO A 2946
REMARK 800
REMARK 800 SITE_IDENTIFIER: AC5
REMARK 800 EVIDENCE_CODE: SOFTWARE
REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE DIO A 2948
DBREF 3NPE A 76 604 UNP O24592 NCED1_MAIZE 76 604
SEQRES 1 A 529 LYS ALA GLU GLY GLY LYS LYS GLN LEU ASN LEU PHE GLN
SEQRES 2 A 529 ARG ALA ALA ALA ALA ALA LEU ASP ALA PHE GLU GLU GLY
SEQRES 3 A 529 PHE VAL ALA ASN VAL LEU GLU ARG PRO HIS GLY LEU PRO
SEQRES 4 A 529 SER THR ALA ASP PRO ALA VAL GLN ILE ALA GLY ASN PHE
SEQRES 5 A 529 ALA PRO VAL GLY GLU ARG PRO PRO VAL HIS GLU LEU PRO
SEQRES 6 A 529 VAL SER GLY ARG ILE PRO PRO PHE ILE ASP GLY VAL TYR
SEQRES 7 A 529 ALA ARG ASN GLY ALA ASN PRO CYS PHE ASP PRO VAL ALA
SEQRES 8 A 529 GLY HIS HIS LEU PHE ASP GLY ASP GLY MET VAL HIS ALA
SEQRES 9 A 529 LEU ARG ILE ARG ASN GLY ALA ALA GLU SER TYR ALA CYS
SEQRES 10 A 529 ARG PHE THR GLU THR ALA ARG LEU ARG GLN GLU ARG ALA
SEQRES 11 A 529 ILE GLY ARG PRO VAL PHE PRO LYS ALA ILE GLY GLU LEU
SEQRES 12 A 529 HIS GLY HIS SER GLY ILE ALA ARG LEU ALA LEU PHE TYR
SEQRES 13 A 529 ALA ARG ALA ALA CYS GLY LEU VAL ASP PRO SER ALA GLY
SEQRES 14 A 529 THR GLY VAL ALA ASN ALA GLY LEU VAL TYR PHE ASN GLY
SEQRES 15 A 529 ARG LEU LEU ALA MET SER GLU ASP ASP LEU PRO TYR HIS
SEQRES 16 A 529 VAL ARG VAL ALA ASP ASP GLY ASP LEU GLU THR VAL GLY
SEQRES 17 A 529 ARG TYR ASP PHE ASP GLY GLN LEU GLY CYS ALA MET ILE
SEQRES 18 A 529 ALA HIS PRO LYS LEU ASP PRO ALA THR GLY GLU LEU HIS
SEQRES 19 A 529 ALA LEU SER TYR ASP VAL ILE LYS ARG PRO TYR LEU LYS
SEQRES 20 A 529 TYR PHE TYR PHE ARG PRO ASP GLY THR LYS SER ASP ASP
SEQRES 21 A 529 VAL GLU ILE PRO LEU GLU GLN PRO THR MET ILE HIS ASP
SEQRES 22 A 529 PHE ALA ILE THR GLU ASN LEU VAL VAL VAL PRO ASP HIS
SEQRES 23 A 529 GLN VAL VAL PHE LYS LEU GLN GLU MET LEU ARG GLY GLY
SEQRES 24 A 529 SER PRO VAL VAL LEU ASP ALA ALA LYS THR SER ARG PHE
SEQRES 25 A 529 GLY VAL LEU PRO LYS HIS ALA ALA ASP ALA SER GLU MET
SEQRES 26 A 529 ALA TRP VAL ASP VAL PRO ASP CYS PHE CYS PHE HIS LEU
SEQRES 27 A 529 TRP ASN ALA TRP GLU ASP GLU ALA THR GLY GLU VAL VAL
SEQRES 28 A 529 VAL ILE GLY SER CYS MET THR PRO ALA ASP SER ILE PHE
SEQRES 29 A 529 ASN GLU SER ASP GLU ARG LEU GLU SER VAL LEU THR GLU
SEQRES 30 A 529 ILE ARG LEU ASP ALA ARG THR GLY ARG SER THR ARG ARG
SEQRES 31 A 529 ALA VAL LEU PRO PRO SER GLN GLN VAL ASN LEU GLU VAL
SEQRES 32 A 529 GLY MET VAL ASN ARG ASN LEU LEU GLY ARG GLU THR ARG
SEQRES 33 A 529 TYR ALA TYR LEU ALA VAL ALA GLU PRO TRP PRO LYS VAL
SEQRES 34 A 529 SER GLY PHE ALA LYS VAL ASP LEU SER THR GLY GLU LEU
SEQRES 35 A 529 THR LYS PHE GLU TYR GLY GLU GLY ARG PHE GLY GLY GLU
SEQRES 36 A 529 PRO CYS PHE VAL PRO MET ASP PRO ALA ALA ALA HIS PRO
SEQRES 37 A 529 ARG GLY GLU ASP ASP GLY TYR VAL LEU THR PHE VAL HIS
SEQRES 38 A 529 ASP GLU ARG ALA GLY THR SER GLU LEU LEU VAL VAL ASN
SEQRES 39 A 529 ALA ALA ASP MET ARG LEU GLU ALA THR VAL GLN LEU PRO
SEQRES 40 A 529 SER ARG VAL PRO PHE GLY PHE HIS GLY THR PHE ILE THR
SEQRES 41 A 529 GLY GLN GLU LEU GLU ALA GLN ALA ALA
HET FE2 A 605 1
HET OXY A 1 2
HET OH A 2 1
HET DIO A2946 6
HET DIO A2947 6
HET DIO A2948 6
HETNAM FE2 FE (II) ION
HETNAM OXY OXYGEN MOLECULE
HETNAM OH HYDROXIDE ION
HETNAM DIO 1,4-DIETHYLENE DIOXIDE
FORMUL 2 FE2 FE 2+
FORMUL 3 OXY O2
FORMUL 4 OH H O 1-
FORMUL 5 DIO 3(C4 H8 O2)
FORMUL 8 HOH *10(H2 O)
HELIX 1 1 LEU A 86 PHE A 102 1 17
HELIX 2 2 ASP A 118 ILE A 123 1 6
HELIX 3 3 ALA A 124 ALA A 128 5 5
HELIX 4 4 HIS A 169 GLY A 173 5 5
HELIX 5 5 THR A 197 GLY A 207 1 11
HELIX 6 6 SER A 222 CYS A 236 1 15
HELIX 7 7 ASP A 240 GLY A 244 5 5
HELIX 8 8 ASP A 286 GLN A 290 5 5
HELIX 9 9 LEU A 367 LEU A 371 5 5
HELIX 10 10 ASP A 396 MET A 400 5 5
HELIX 11 11 ARG A 483 LEU A 486 5 4
HELIX 12 12 GLY A 596 GLU A 600 1 5
SHEET 1 A 5 ARG A 133 HIS A 137 0
SHEET 2 A 5 ALA A 186 PHE A 194 -1 O CYS A 192 N ARG A 133
SHEET 3 A 5 MET A 176 ARG A 183 -1 N VAL A 177 O ARG A 193
SHEET 4 A 5 ASP A 150 ARG A 155 -1 N GLY A 151 O ILE A 182
SHEET 5 A 5 GLY A 591 THR A 595 -1 O THR A 592 N ALA A 154
SHEET 1 B 5 VAL A 141 GLY A 143 0
SHEET 2 B 5 ARG A 574 LEU A 581 -1 O THR A 578 N SER A 142
SHEET 3 B 5 SER A 563 ASN A 569 -1 N SER A 563 O LEU A 581
SHEET 4 B 5 GLY A 549 HIS A 556 -1 N THR A 553 O LEU A 566
SHEET 5 B 5 CYS A 532 PRO A 535 -1 N VAL A 534 O TYR A 550
SHEET 1 C 4 LEU A 252 PHE A 255 0
SHEET 2 C 4 ARG A 258 ALA A 261 -1 O ARG A 258 N PHE A 255
SHEET 3 C 4 TYR A 269 VAL A 273 -1 O TYR A 269 N ALA A 261
SHEET 4 C 4 LEU A 279 ARG A 284 -1 O GLU A 280 N ARG A 272
SHEET 1 D 4 LYS A 300 LEU A 301 0
SHEET 2 D 4 LEU A 308 SER A 312 -1 O HIS A 309 N LYS A 300
SHEET 3 D 4 LYS A 322 PHE A 326 -1 O LYS A 322 N SER A 312
SHEET 4 D 4 VAL A 336 GLU A 337 -1 O VAL A 336 N TYR A 323
SHEET 1 E 4 ALA A 350 ILE A 351 0
SHEET 2 E 4 LEU A 355 ASP A 360 -1 O VAL A 357 N ALA A 350
SHEET 3 E 4 ARG A 386 PRO A 391 -1 O LEU A 390 N VAL A 356
SHEET 4 E 4 ALA A 401 ASP A 404 -1 O VAL A 403 N PHE A 387
SHEET 1 F 2 VAL A 363 PHE A 365 0
SHEET 2 F 2 VAL A 377 LEU A 379 -1 O VAL A 378 N VAL A 364
SHEET 1 G 4 PHE A 409 GLU A 418 0
SHEET 2 G 4 VAL A 425 MET A 432 -1 O VAL A 426 N TRP A 417
SHEET 3 G 4 VAL A 449 LEU A 455 -1 O THR A 451 N GLY A 429
SHEET 4 G 4 SER A 462 ALA A 466 -1 O ARG A 465 N GLU A 452
SHEET 1 H 4 LEU A 476 VAL A 481 0
SHEET 2 H 4 TYR A 492 VAL A 497 -1 O TYR A 494 N MET A 480
SHEET 3 H 4 GLY A 506 ASP A 511 -1 O VAL A 510 N ALA A 493
SHEET 4 H 4 LEU A 517 GLU A 521 -1 O PHE A 520 N PHE A 507
SSBOND 1 CYS A 410 CYS A 431 1555 1555 2.06
LINK O2 OXY A 1 FE FE2 A 605 1555 1555 2.04
LINK O OH A 2 FE FE2 A 605 1555 1555 2.05
LINK NE2 HIS A 298 FE FE2 A 605 1555 1555 1.86
LINK NE2 HIS A 347 FE FE2 A 605 1555 1555 1.88
LINK NE2 HIS A 412 FE FE2 A 605 1555 1555 1.87
LINK NE2 HIS A 590 FE FE2 A 605 1555 1555 1.89
SITE 1 AC1 6 OXY A 1 OH A 2 HIS A 298 HIS A 347
SITE 2 AC1 6 HIS A 412 HIS A 590
SITE 1 AC2 5 OH A 2 HIS A 347 HIS A 412 HIS A 590
SITE 2 AC2 5 FE2 A 605
SITE 1 AC3 5 OXY A 1 HIS A 298 HIS A 347 HIS A 590
SITE 2 AC3 5 FE2 A 605
SITE 1 AC4 2 PRO A 134 ARG A 193
SITE 1 AC5 2 PHE A 162 ASP A 163
CRYST1 161.521 161.521 150.816 90.00 90.00 120.00 P 63 2 2 12
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 0.006191 0.003574 0.000000 0.00000
SCALE2 0.000000 0.007149 0.000000 0.00000
SCALE3 0.000000 0.000000 0.006631 0.00000
(ATOM LINES ARE NOT SHOWN.)
END
