HEADER LYASE 13-MAY-16 5G4J
TITLE PHOSPHOLYASE A1RDF1 FROM ARTHROBACTER IN COMPLEX WITH
TITLE 2 PHOSPHOETHANOLAMINE
COMPND MOL_ID: 1;
COMPND 2 MOLECULE: PUTATIVE AMINOTRANSFERASE CLASS III PROTEIN;
COMPND 3 CHAIN: A, B;
COMPND 4 EC: 4.2.3.2;
COMPND 5 ENGINEERED: YES
SOURCE MOL_ID: 1;
SOURCE 2 ORGANISM_SCIENTIFIC: ARTHROBACTER AURESCENS;
SOURCE 3 ORGANISM_TAXID: 290340;
SOURCE 4 STRAIN: TC1;
SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI;
SOURCE 6 EXPRESSION_SYSTEM_TAXID: 469008;
SOURCE 7 EXPRESSION_SYSTEM_STRAIN: BL21(DE3);
SOURCE 8 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID;
SOURCE 9 EXPRESSION_SYSTEM_PLASMID: PET-YSBLIC-3C
KEYWDS LYASE, PYRIDOXAL PHOSPHATE, TRANSAMINASE, PHOSPHOLYASE
EXPDTA X-RAY DIFFRACTION
AUTHOR A.CUETOS,A.N.TUAN,J.MANGAS SANCHEZ,G.GROGAN
REVDAT 3 10-JAN-24 5G4J 1 REMARK LINK
REVDAT 2 01-MAR-17 5G4J 1 JRNL
REVDAT 1 19-OCT-16 5G4J 0
JRNL AUTH A.CUETOS,F.STEFFEN-MUNSBERG,J.MANGAS SANCHEZ,A.FRESE,
JRNL AUTH 2 U.T.BORNSCHEUER,M.HOHNE,G.GROGAN
JRNL TITL STRUCTURAL BASIS FOR PHOSPHOLYASE ACTIVITY OF A CLASS III
JRNL TITL 2 TRANSAMINASE HOMOLOGUE.
JRNL REF CHEMBIOCHEM V. 17 2308 2016
JRNL REFN ESSN 1439-7633
JRNL PMID 27709756
JRNL DOI 10.1002/CBIC.201600482
REMARK 2
REMARK 2 RESOLUTION. 1.87 ANGSTROMS.
REMARK 3
REMARK 3 REFINEMENT.
REMARK 3 PROGRAM : REFMAC 5.8.0135
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) : 1.87
REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 75.60
REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL
REMARK 3 COMPLETENESS FOR RANGE (%) : 99.8
REMARK 3 NUMBER OF REFLECTIONS : 70978
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) : 0.169
REMARK 3 R VALUE (WORKING SET) : 0.167
REMARK 3 FREE R VALUE : 0.199
REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.900
REMARK 3 FREE R VALUE TEST SET COUNT : 3636
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) : 1.87
REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.92
REMARK 3 REFLECTION IN BIN (WORKING SET) : 5226
REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 99.84
REMARK 3 BIN R VALUE (WORKING SET) : 0.2420
REMARK 3 BIN FREE R VALUE SET COUNT : 240
REMARK 3 BIN FREE R VALUE : 0.2680
REMARK 3
REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT.
REMARK 3 PROTEIN ATOMS : 6300
REMARK 3 NUCLEIC ACID ATOMS : 0
REMARK 3 HETEROGEN ATOMS : 49
REMARK 3 SOLVENT ATOMS : 476
REMARK 3
REMARK 3 B VALUES.
REMARK 3 FROM WILSON PLOT (A**2) : NULL
REMARK 3 MEAN B VALUE (OVERALL, A**2) : 25.91
REMARK 3 OVERALL ANISOTROPIC B VALUE.
REMARK 3 B11 (A**2) : -1.84000
REMARK 3 B22 (A**2) : 0.51000
REMARK 3 B33 (A**2) : 1.32000
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): 0.126
REMARK 3 ESU BASED ON FREE R VALUE (A): 0.118
REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.081
REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 2.770
REMARK 3
REMARK 3 CORRELATION COEFFICIENTS.
REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.963
REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.949
REMARK 3
REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT
REMARK 3 BOND LENGTHS REFINED ATOMS (A): 6494 ; 0.021 ; 0.019
REMARK 3 BOND LENGTHS OTHERS (A): 6175 ; 0.008 ; 0.020
REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 8831 ; 1.915 ; 1.975
REMARK 3 BOND ANGLES OTHERS (DEGREES): 14127 ; 1.478 ; 3.001
REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 847 ; 6.287 ; 5.000
REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 259 ;32.885 ;23.282
REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 998 ;14.118 ;15.000
REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 47 ;18.596 ;15.000
REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 1015 ; 0.227 ; 0.200
REMARK 3 GENERAL PLANES REFINED ATOMS (A): 7445 ; 0.012 ; 0.021
REMARK 3 GENERAL PLANES OTHERS (A): 1477 ; 0.006 ; 0.020
REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): NULL ; NULL ; NULL
REMARK 3 NON-BONDED CONTACTS OTHERS (A): NULL ; NULL ; NULL
REMARK 3 NON-BONDED TORSION REFINED ATOMS (A): NULL ; NULL ; NULL
REMARK 3 NON-BONDED TORSION OTHERS (A): NULL ; NULL ; NULL
REMARK 3 H-BOND (X...Y) REFINED ATOMS (A): NULL ; NULL ; NULL
REMARK 3 H-BOND (X...Y) OTHERS (A): NULL ; NULL ; NULL
REMARK 3 POTENTIAL METAL-ION REFINED ATOMS (A): NULL ; NULL ; NULL
REMARK 3 POTENTIAL METAL-ION OTHERS (A): NULL ; NULL ; NULL
REMARK 3 SYMMETRY VDW REFINED ATOMS (A): NULL ; NULL ; NULL
REMARK 3 SYMMETRY VDW OTHERS (A): NULL ; NULL ; NULL
REMARK 3 SYMMETRY H-BOND REFINED ATOMS (A): NULL ; NULL ; NULL
REMARK 3 SYMMETRY H-BOND OTHERS (A): NULL ; NULL ; NULL
REMARK 3 SYMMETRY METAL-ION REFINED ATOMS (A): NULL ; NULL ; NULL
REMARK 3 SYMMETRY METAL-ION OTHERS (A): NULL ; NULL ; NULL
REMARK 3
REMARK 3 ISOTROPIC THERMAL FACTOR RESTRAINTS. COUNT RMS WEIGHT
REMARK 3 MAIN-CHAIN BOND REFINED ATOMS (A**2): 3382 ; 2.382 ; 2.468
REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): 3381 ; 2.381 ; 2.466
REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 4225 ; 3.081 ; 3.684
REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL
REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 3112 ; 3.127 ; 2.735
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 : NULL
REMARK 3 PARAMETERS FOR MASK CALCULATION
REMARK 3 VDW PROBE RADIUS : 1.20
REMARK 3 ION PROBE RADIUS : 0.80
REMARK 3 SHRINKAGE RADIUS : 0.80
REMARK 3
REMARK 3 OTHER REFINEMENT REMARKS: HYDROGENS HAVE BEEN ADDED IN THE RIDING
REMARK 3 POSITIONS.
REMARK 4
REMARK 4 5G4J COMPLIES WITH FORMAT V. 3.30, 13-JUL-11
REMARK 100
REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 13-MAY-16.
REMARK 100 THE DEPOSITION ID IS D_1290066848.
REMARK 200
REMARK 200 EXPERIMENTAL DETAILS
REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION
REMARK 200 DATE OF DATA COLLECTION : 18-APR-16
REMARK 200 TEMPERATURE (KELVIN) : 120
REMARK 200 PH : 6
REMARK 200 NUMBER OF CRYSTALS USED : 1
REMARK 200
REMARK 200 SYNCHROTRON (Y/N) : Y
REMARK 200 RADIATION SOURCE : DIAMOND
REMARK 200 BEAMLINE : I02
REMARK 200 X-RAY GENERATOR MODEL : NULL
REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M
REMARK 200 WAVELENGTH OR RANGE (A) : 0.9795
REMARK 200 MONOCHROMATOR : NULL
REMARK 200 OPTICS : NULL
REMARK 200
REMARK 200 DETECTOR TYPE : PIXEL
REMARK 200 DETECTOR MANUFACTURER : DECTRIS PILATUS 6M
REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS
REMARK 200 DATA SCALING SOFTWARE : SCALA
REMARK 200
REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 74689
REMARK 200 RESOLUTION RANGE HIGH (A) : 1.870
REMARK 200 RESOLUTION RANGE LOW (A) : 64.590
REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 2.000
REMARK 200
REMARK 200 OVERALL.
REMARK 200 COMPLETENESS FOR RANGE (%) : 99.8
REMARK 200 DATA REDUNDANCY : 6.500
REMARK 200 R MERGE (I) : 0.08000
REMARK 200 R SYM (I) : NULL
REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 14.5000
REMARK 200
REMARK 200 IN THE HIGHEST RESOLUTION SHELL.
REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.87
REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.95
REMARK 200 COMPLETENESS FOR SHELL (%) : 99.9
REMARK 200 DATA REDUNDANCY IN SHELL : 6.80
REMARK 200 R MERGE FOR SHELL (I) : 0.67000
REMARK 200 R SYM FOR SHELL (I) : NULL
REMARK 200 <I/SIGMA(I)> FOR SHELL : 2.600
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: PDB ENTRY 5G4I
REMARK 200
REMARK 200 REMARK: NONE
REMARK 280
REMARK 280 CRYSTAL
REMARK 280 SOLVENT CONTENT, VS (%): 47.00
REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.33
REMARK 280
REMARK 280 CRYSTALLIZATION CONDITIONS: 24% (W/V) PEG 3350, 0.2 M (NH4)2SO4
REMARK 280 AND 3% (V/V) 2-METHYL-2,4-PENTANEDIOL IN 0.1 M BIS-TRIS PROPANE
REMARK 280 BUFFER AT PH 6.0
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 38.08300
REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000
REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 60.94850
REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000
REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 48.18550
REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 60.94850
REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 38.08300
REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 48.18550
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
REMARK 350 TOTAL BURIED SURFACE AREA: 10930 ANGSTROM**2
REMARK 350 SURFACE AREA OF THE COMPLEX: 27110 ANGSTROM**2
REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -90.7 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 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 THR A 2
REMARK 465 SER A 3
REMARK 465 GLU A 4
REMARK 465 THR A 5
REMARK 465 THR A 6
REMARK 465 THR A 7
REMARK 465 THR A 8
REMARK 465 PRO A 9
REMARK 465 SER A 10
REMARK 465 ARG A 11
REMARK 465 VAL A 12
REMARK 465 PRO A 13
REMARK 465 GLN A 14
REMARK 465 THR A 15
REMARK 465 ALA A 16
REMARK 465 ASN A 17
REMARK 465 PRO A 441
REMARK 465 GLY A 442
REMARK 465 ASN A 443
REMARK 465 LEU A 444
REMARK 465 VAL A 445
REMARK 465 LEU A 446
REMARK 465 MET B 1
REMARK 465 THR B 2
REMARK 465 SER B 3
REMARK 465 GLU B 4
REMARK 465 THR B 5
REMARK 465 THR B 6
REMARK 465 THR B 7
REMARK 465 THR B 8
REMARK 465 PRO B 9
REMARK 465 SER B 10
REMARK 465 ARG B 11
REMARK 465 VAL B 12
REMARK 465 PRO B 13
REMARK 465 GLN B 14
REMARK 465 THR B 15
REMARK 465 ALA B 16
REMARK 465 ASN B 17
REMARK 465 GLN B 440
REMARK 465 PRO B 441
REMARK 465 GLY B 442
REMARK 465 ASN B 443
REMARK 465 LEU B 444
REMARK 465 VAL B 445
REMARK 465 LEU B 446
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 ASP A 18 CG OD1 OD2
REMARK 470 ARG A 36 CD NE CZ NH1 NH2
REMARK 470 ARG A 175 NH1 NH2
REMARK 470 ILE A 182 CG2 CD1
REMARK 470 ALA A 183 CB
REMARK 470 GLU A 184 CG CD OE1 OE2
REMARK 470 GLU A 192 CD OE1 OE2
REMARK 470 GLN A 193 NE2
REMARK 470 GLN A 228 CD OE1 NE2
REMARK 470 GLU A 297 CD OE1 OE2
REMARK 470 ARG A 327 NH2
REMARK 470 GLN A 331 CG CD OE1 NE2
REMARK 470 GLN A 340 OE1 NE2
REMARK 470 LYS A 347 CD CE NZ
REMARK 470 GLN A 354 CD OE1 NE2
REMARK 470 ARG A 380 NE CZ NH1 NH2
REMARK 470 LYS A 388 CE NZ
REMARK 470 ARG A 421 NH2
REMARK 470 GLU A 422 OE2
REMARK 470 GLN A 440 CG CD OE1 NE2
REMARK 470 ASP B 18 CG OD1 OD2
REMARK 470 LEU B 20 CD2
REMARK 470 ARG B 36 CD NE CZ NH1 NH2
REMARK 470 GLN B 37 CD OE1 NE2
REMARK 470 GLN B 53 CG CD OE1 NE2
REMARK 470 ARG B 175 NH1 NH2
REMARK 470 ILE B 182 CD1
REMARK 470 VAL B 189 CG1
REMARK 470 GLU B 192 CD OE1 OE2
REMARK 470 GLN B 193 CD OE1 NE2
REMARK 470 GLN B 228 CD OE1 NE2
REMARK 470 GLU B 235 CD OE1 OE2
REMARK 470 ASN B 271 ND2
REMARK 470 GLU B 297 CD OE1 OE2
REMARK 470 ARG B 327 NH2
REMARK 470 GLN B 331 NE2
REMARK 470 GLN B 340 CD OE1 NE2
REMARK 470 LYS B 343 CE NZ
REMARK 470 LYS B 347 NZ
REMARK 470 ASN B 351 OD1 ND2
REMARK 470 ILE B 352 CD1
REMARK 470 GLN B 354 CG CD OE1 NE2
REMARK 470 ARG B 355 CZ NH1 NH2
REMARK 470 ARG B 380 CG CD NE CZ NH1 NH2
REMARK 470 ASN B 381 CG OD1 ND2
REMARK 470 LYS B 388 CD CE NZ
REMARK 470 GLU B 396 CG CD OE1 OE2
REMARK 470 GLU B 422 CG CD OE1 OE2
REMARK 470 PRO B 439 CG
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 OE1 GLU A 98 O HOH A 2088 2.13
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 76 CB - CG - OD1 ANGL. DEV. = 7.2 DEGREES
REMARK 500 ASP A 108 CB - CA - C ANGL. DEV. = -14.2 DEGREES
REMARK 500 ASP A 108 CB - CG - OD2 ANGL. DEV. = -6.8 DEGREES
REMARK 500 LEU A 161 CA - CB - CG ANGL. DEV. = 16.2 DEGREES
REMARK 500 LEU A 323 CA - CB - CG ANGL. DEV. = 15.6 DEGREES
REMARK 500 ARG A 346 NE - CZ - NH1 ANGL. DEV. = 6.8 DEGREES
REMARK 500 ARG A 346 NE - CZ - NH2 ANGL. DEV. = -6.1 DEGREES
REMARK 500 ARG A 348 CG - CD - NE ANGL. DEV. = -14.1 DEGREES
REMARK 500 ARG A 348 NE - CZ - NH1 ANGL. DEV. = 4.2 DEGREES
REMARK 500 ARG A 348 NE - CZ - NH2 ANGL. DEV. = -5.8 DEGREES
REMARK 500 ARG A 365 NE - CZ - NH1 ANGL. DEV. = 4.0 DEGREES
REMARK 500 ARG A 365 NE - CZ - NH2 ANGL. DEV. = -7.4 DEGREES
REMARK 500 LEU B 161 CA - CB - CG ANGL. DEV. = 18.1 DEGREES
REMARK 500 MET B 283 CG - SD - CE ANGL. DEV. = -10.3 DEGREES
REMARK 500 ARG B 346 CG - CD - NE ANGL. DEV. = -13.1 DEGREES
REMARK 500 ARG B 346 NE - CZ - NH1 ANGL. DEV. = 5.9 DEGREES
REMARK 500 ARG B 346 NE - CZ - NH2 ANGL. DEV. = -5.6 DEGREES
REMARK 500 ARG B 348 NE - CZ - NH1 ANGL. DEV. = 4.2 DEGREES
REMARK 500 ARG B 348 NE - CZ - NH2 ANGL. DEV. = -4.4 DEGREES
REMARK 500 ARG B 365 NE - CZ - NH1 ANGL. DEV. = 3.4 DEGREES
REMARK 500 ARG B 365 NE - CZ - NH2 ANGL. DEV. = -5.3 DEGREES
REMARK 500 ARG B 395 NE - CZ - NH1 ANGL. DEV. = 5.3 DEGREES
REMARK 500 ARG B 395 NE - CZ - NH2 ANGL. DEV. = -5.8 DEGREES
REMARK 500
REMARK 500 REMARK: NULL
REMARK 500
REMARK 500 GEOMETRY AND STEREOCHEMISTRY
REMARK 500 SUBTOPIC: TORSION ANGLES
REMARK 500
REMARK 500 TORSION ANGLES OUTSIDE THE EXPECTED RAMACHANDRAN REGIONS:
REMARK 500 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER;
REMARK 500 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE).
REMARK 500
REMARK 500 STANDARD TABLE:
REMARK 500 FORMAT:(10X,I3,1X,A3,1X,A1,I4,A1,4X,F7.2,3X,F7.2)
REMARK 500
REMARK 500 EXPECTED VALUES: GJ KLEYWEGT AND TA JONES (1996). PHI/PSI-
REMARK 500 CHOLOGY: RAMACHANDRAN REVISITED. STRUCTURE 4, 1395 - 1400
REMARK 500
REMARK 500 M RES CSSEQI PSI PHI
REMARK 500 THR A 26 -62.38 -126.00
REMARK 500 TYR A 35 159.20 79.26
REMARK 500 TYR A 61 -35.16 -133.91
REMARK 500 THR A 84 -72.22 -114.29
REMARK 500 ASN A 86 52.30 -143.87
REMARK 500 GLU A 112 18.84 -144.66
REMARK 500 PHE A 145 70.14 -154.08
REMARK 500 LYS A 281 -94.49 4.53
REMARK 500 ALA A 383 76.64 -116.02
REMARK 500 ARG A 414 68.05 -159.40
REMARK 500 THR B 26 -64.63 -122.05
REMARK 500 TYR B 35 156.51 78.10
REMARK 500 TYR B 61 -39.24 -132.84
REMARK 500 THR B 84 -73.26 -115.51
REMARK 500 ASN B 86 56.64 -147.42
REMARK 500 GLU B 112 19.71 -144.44
REMARK 500 PHE B 145 71.41 -150.12
REMARK 500 LYS B 281 -96.42 7.23
REMARK 500 ALA B 383 78.98 -114.33
REMARK 500 ARG B 414 71.34 -160.98
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 NA A1443 NA
REMARK 620 N RES CSSEQI ATOM
REMARK 620 1 ALA A 353 O
REMARK 620 2 SER A 356 O 87.8
REMARK 620 3 VAL A 359 O 117.8 97.2
REMARK 620 4 HOH A2285 O 93.4 174.6 77.5
REMARK 620 N 1 2 3
REMARK 800
REMARK 800 SITE
REMARK 800 SITE_IDENTIFIER: AC1
REMARK 800 EVIDENCE_CODE: SOFTWARE
REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE EXT B 1440
REMARK 800
REMARK 800 SITE_IDENTIFIER: AC2
REMARK 800 EVIDENCE_CODE: SOFTWARE
REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE EXT A 1441
REMARK 800
REMARK 800 SITE_IDENTIFIER: AC3
REMARK 800 EVIDENCE_CODE: SOFTWARE
REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE NA A 1442
REMARK 800
REMARK 800 SITE_IDENTIFIER: AC4
REMARK 800 EVIDENCE_CODE: SOFTWARE
REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE NA B 1441
REMARK 800
REMARK 800 SITE_IDENTIFIER: AC5
REMARK 800 EVIDENCE_CODE: SOFTWARE
REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE NA A 1443
REMARK 900
REMARK 900 RELATED ENTRIES
REMARK 900 RELATED ID: 5G4I RELATED DB: PDB
REMARK 900 PLP-DEPENDENT PHOSPHOLYASE A1RDF1 FROM ARTHROBACTER AURESCENS TC1
DBREF 5G4J A 1 446 UNP A1RDF1 A1RDF1_ARTAT 1 446
DBREF 5G4J B 1 446 UNP A1RDF1 A1RDF1_ARTAT 1 446
SEQRES 1 A 446 MET THR SER GLU THR THR THR THR PRO SER ARG VAL PRO
SEQRES 2 A 446 GLN THR ALA ASN ASP LEU LEU ALA ARG ARG TYR ALA THR
SEQRES 3 A 446 ILE GLY PRO HIS SER PRO LEU PHE TYR ARG GLN PRO LEU
SEQRES 4 A 446 GLU LEU VAL SER GLY SER GLY VAL TRP LEU THR ASP ALA
SEQRES 5 A 446 GLN GLY LYS VAL TYR LEU ASP GLY TYR ASN ASN VAL PRO
SEQRES 6 A 446 HIS VAL GLY HIS ALA ASN PRO ALA VAL ALA ASP ALA ILE
SEQRES 7 A 446 TYR GLN GLN LEU LEU THR VAL ASN LEU HIS THR ARG TYR
SEQRES 8 A 446 LEU ASN SER ARG VAL VAL GLU TYR ALA GLU ALA LEU LEU
SEQRES 9 A 446 SER LYS PHE ASP GLY ALA LEU GLU ARG LEU PHE LEU THR
SEQRES 10 A 446 ASN SER GLY SER GLU ALA ASN GLU LEU ALA LEU ARG ILE
SEQRES 11 A 446 ALA ARG GLN HIS THR GLY ASN THR GLY VAL LEU VAL SER
SEQRES 12 A 446 ASP PHE SER TYR HIS GLY ASN THR THR SER LEU ALA GLU
SEQRES 13 A 446 ILE THR THR GLY LEU THR VAL HIS GLU PRO LEU GLY ALA
SEQRES 14 A 446 HIS VAL ARG ALA LEU ARG ILE PRO ASP VAL SER GLY ILE
SEQRES 15 A 446 ALA GLU VAL ASP VAL PRO VAL LEU LEU GLU GLN SER LEU
SEQRES 16 A 446 ALA ASP VAL ASP ALA ALA ILE ALA SER LEU GLN ALA ALA
SEQRES 17 A 446 GLY HIS GLY VAL SER VAL PHE LEU PHE ASP PRO LEU PHE
SEQRES 18 A 446 SER THR GLU GLY LEU LEU GLN LEU PRO SER GLY TYR ILE
SEQRES 19 A 446 GLU GLY VAL ALA THR ARG VAL ARG ALA ALA GLY GLY LEU
SEQRES 20 A 446 VAL ILE SER ASP GLU VAL GLN SER GLY PHE GLY ARG THR
SEQRES 21 A 446 GLY SER GLY MET TRP GLY TYR GLN MET PHE ASN VAL GLU
SEQRES 22 A 446 PRO GLU LEU VAL THR MET GLY LYS PRO MET GLY ASN GLY
SEQRES 23 A 446 HIS PRO ILE GLY ALA VAL VAL THR THR ALA GLU LEU LEU
SEQRES 24 A 446 ASP GLU PHE GLY ARG HIS ASN MET PHE PHE ASN THR PHE
SEQRES 25 A 446 ALA GLY ASN PRO VAL SER SER ALA ALA GLY LEU ALA VAL
SEQRES 26 A 446 LEU ARG TYR MET ASP GLN GLU ASP LEU MET ALA LYS ALA
SEQRES 27 A 446 ASP GLN LEU GLY LYS TYR ILE ARG LYS ARG LEU GLU ASN
SEQRES 28 A 446 ILE ALA GLN ARG SER GLY ASN VAL GLY SER VAL ARG GLY
SEQRES 29 A 446 ARG GLY LEU PHE PHE GLY ILE ASP ILE ILE GLU SER ASP
SEQRES 30 A 446 GLY SER ARG ASN PRO ALA PRO ALA LEU THR LYS ILE LEU
SEQRES 31 A 446 ILE GLU ASP MET ARG GLU ARG GLY VAL LEU ILE SER ARG
SEQRES 32 A 446 VAL GLY PRO HIS ASP ASN VAL LEU LYS MET ARG PRO PRO
SEQRES 33 A 446 LEU VAL PHE GLY ARG GLU HIS ALA ASP ILE LEU LEU GLY
SEQRES 34 A 446 GLN LEU GLU LEU SER LEU ALA SER LEU PRO GLN PRO GLY
SEQRES 35 A 446 ASN LEU VAL LEU
SEQRES 1 B 446 MET THR SER GLU THR THR THR THR PRO SER ARG VAL PRO
SEQRES 2 B 446 GLN THR ALA ASN ASP LEU LEU ALA ARG ARG TYR ALA THR
SEQRES 3 B 446 ILE GLY PRO HIS SER PRO LEU PHE TYR ARG GLN PRO LEU
SEQRES 4 B 446 GLU LEU VAL SER GLY SER GLY VAL TRP LEU THR ASP ALA
SEQRES 5 B 446 GLN GLY LYS VAL TYR LEU ASP GLY TYR ASN ASN VAL PRO
SEQRES 6 B 446 HIS VAL GLY HIS ALA ASN PRO ALA VAL ALA ASP ALA ILE
SEQRES 7 B 446 TYR GLN GLN LEU LEU THR VAL ASN LEU HIS THR ARG TYR
SEQRES 8 B 446 LEU ASN SER ARG VAL VAL GLU TYR ALA GLU ALA LEU LEU
SEQRES 9 B 446 SER LYS PHE ASP GLY ALA LEU GLU ARG LEU PHE LEU THR
SEQRES 10 B 446 ASN SER GLY SER GLU ALA ASN GLU LEU ALA LEU ARG ILE
SEQRES 11 B 446 ALA ARG GLN HIS THR GLY ASN THR GLY VAL LEU VAL SER
SEQRES 12 B 446 ASP PHE SER TYR HIS GLY ASN THR THR SER LEU ALA GLU
SEQRES 13 B 446 ILE THR THR GLY LEU THR VAL HIS GLU PRO LEU GLY ALA
SEQRES 14 B 446 HIS VAL ARG ALA LEU ARG ILE PRO ASP VAL SER GLY ILE
SEQRES 15 B 446 ALA GLU VAL ASP VAL PRO VAL LEU LEU GLU GLN SER LEU
SEQRES 16 B 446 ALA ASP VAL ASP ALA ALA ILE ALA SER LEU GLN ALA ALA
SEQRES 17 B 446 GLY HIS GLY VAL SER VAL PHE LEU PHE ASP PRO LEU PHE
SEQRES 18 B 446 SER THR GLU GLY LEU LEU GLN LEU PRO SER GLY TYR ILE
SEQRES 19 B 446 GLU GLY VAL ALA THR ARG VAL ARG ALA ALA GLY GLY LEU
SEQRES 20 B 446 VAL ILE SER ASP GLU VAL GLN SER GLY PHE GLY ARG THR
SEQRES 21 B 446 GLY SER GLY MET TRP GLY TYR GLN MET PHE ASN VAL GLU
SEQRES 22 B 446 PRO GLU LEU VAL THR MET GLY LYS PRO MET GLY ASN GLY
SEQRES 23 B 446 HIS PRO ILE GLY ALA VAL VAL THR THR ALA GLU LEU LEU
SEQRES 24 B 446 ASP GLU PHE GLY ARG HIS ASN MET PHE PHE ASN THR PHE
SEQRES 25 B 446 ALA GLY ASN PRO VAL SER SER ALA ALA GLY LEU ALA VAL
SEQRES 26 B 446 LEU ARG TYR MET ASP GLN GLU ASP LEU MET ALA LYS ALA
SEQRES 27 B 446 ASP GLN LEU GLY LYS TYR ILE ARG LYS ARG LEU GLU ASN
SEQRES 28 B 446 ILE ALA GLN ARG SER GLY ASN VAL GLY SER VAL ARG GLY
SEQRES 29 B 446 ARG GLY LEU PHE PHE GLY ILE ASP ILE ILE GLU SER ASP
SEQRES 30 B 446 GLY SER ARG ASN PRO ALA PRO ALA LEU THR LYS ILE LEU
SEQRES 31 B 446 ILE GLU ASP MET ARG GLU ARG GLY VAL LEU ILE SER ARG
SEQRES 32 B 446 VAL GLY PRO HIS ASP ASN VAL LEU LYS MET ARG PRO PRO
SEQRES 33 B 446 LEU VAL PHE GLY ARG GLU HIS ALA ASP ILE LEU LEU GLY
SEQRES 34 B 446 GLN LEU GLU LEU SER LEU ALA SER LEU PRO GLN PRO GLY
SEQRES 35 B 446 ASN LEU VAL LEU
HET EXT A1441 23
HET NA A1442 1
HET NA A1443 1
HET EXT B1440 23
HET NA B1441 1
HETNAM EXT {5-HYDROXY-6-METHYL-4-[(E)-{[2-(PHOSPHONOOXY)
HETNAM 2 EXT ETHYL]IMINO}METHYL]PYRIDIN-3-YL}METHYL DIHYDROGEN
HETNAM 3 EXT PHOSPHATE
HETNAM NA SODIUM ION
FORMUL 3 EXT 2(C10 H16 N2 O9 P2)
FORMUL 4 NA 3(NA 1+)
FORMUL 8 HOH *476(H2 O)
HELIX 1 1 ASP A 18 ALA A 25 1 8
HELIX 2 2 ASN A 71 LEU A 83 1 13
HELIX 3 3 ASN A 93 SER A 105 1 13
HELIX 4 4 SER A 119 GLY A 136 1 18
HELIX 5 5 THR A 151 GLU A 156 1 6
HELIX 6 6 ALA A 183 VAL A 185 5 3
HELIX 7 7 ASP A 186 ALA A 208 1 23
HELIX 8 8 GLY A 232 ALA A 244 1 13
HELIX 9 9 TRP A 265 PHE A 270 5 6
HELIX 10 10 GLY A 280 ASN A 285 5 6
HELIX 11 11 ALA A 296 ASN A 306 1 11
HELIX 12 12 ASN A 315 GLU A 332 1 18
HELIX 13 13 ASP A 333 SER A 356 1 24
HELIX 14 14 ALA A 383 ARG A 397 1 15
HELIX 15 15 GLY A 420 SER A 437 1 18
HELIX 16 16 ASP B 18 ALA B 25 1 8
HELIX 17 17 ASN B 71 LEU B 83 1 13
HELIX 18 18 ASN B 93 SER B 105 1 13
HELIX 19 19 SER B 119 GLY B 136 1 18
HELIX 20 20 THR B 151 GLU B 156 1 6
HELIX 21 21 ALA B 183 VAL B 185 5 3
HELIX 22 22 ASP B 186 ALA B 208 1 23
HELIX 23 23 GLY B 232 ALA B 244 1 13
HELIX 24 24 TRP B 265 PHE B 270 5 6
HELIX 25 25 GLY B 280 ASN B 285 5 6
HELIX 26 26 THR B 295 ASN B 306 1 12
HELIX 27 27 ASN B 315 GLU B 332 1 18
HELIX 28 28 ASP B 333 SER B 356 1 24
HELIX 29 29 ALA B 383 ARG B 397 1 15
HELIX 30 30 GLY B 420 SER B 437 1 18
SHEET 1 AA 4 LEU A 41 SER A 45 0
SHEET 2 AA 4 TRP A 48 ASP A 51 -1 O TRP A 48 N SER A 45
SHEET 3 AA 4 VAL A 56 ASP A 59 -1 O TYR A 57 N LEU A 49
SHEET 4 AA 4 VAL A 399 LEU A 400 1 N LEU A 400 O LEU A 58
SHEET 1 AB 7 LEU A 111 THR A 117 0
SHEET 2 AB 7 GLY A 290 THR A 295 -1 O GLY A 290 N THR A 117
SHEET 3 AB 7 LEU A 276 MET A 279 -1 O VAL A 277 N VAL A 293
SHEET 4 AB 7 LEU A 247 ASP A 251 1 O VAL A 248 N LEU A 276
SHEET 5 AB 7 VAL A 214 PHE A 217 1 O PHE A 215 N ILE A 249
SHEET 6 AB 7 VAL A 140 SER A 143 1 O LEU A 141 N LEU A 216
SHEET 7 AB 7 VAL A 171 LEU A 174 1 O ARG A 172 N VAL A 142
SHEET 1 AC 4 VAL A 359 ARG A 365 0
SHEET 2 AC 4 PHE A 368 ILE A 373 -1 O PHE A 368 N ARG A 365
SHEET 3 AC 4 VAL A 410 MET A 413 -1 O LEU A 411 N ILE A 371
SHEET 4 AC 4 SER A 402 VAL A 404 -1 O SER A 402 N LYS A 412
SHEET 1 BA 4 LEU B 41 SER B 45 0
SHEET 2 BA 4 TRP B 48 ASP B 51 -1 O TRP B 48 N SER B 45
SHEET 3 BA 4 VAL B 56 ASP B 59 -1 O TYR B 57 N LEU B 49
SHEET 4 BA 4 VAL B 399 LEU B 400 1 N LEU B 400 O LEU B 58
SHEET 1 BB 7 ARG B 113 THR B 117 0
SHEET 2 BB 7 GLY B 290 THR B 294 -1 O GLY B 290 N THR B 117
SHEET 3 BB 7 LEU B 276 MET B 279 -1 O VAL B 277 N VAL B 293
SHEET 4 BB 7 LEU B 247 ASP B 251 1 O VAL B 248 N LEU B 276
SHEET 5 BB 7 VAL B 214 PHE B 217 1 O PHE B 215 N ILE B 249
SHEET 6 BB 7 VAL B 140 SER B 143 1 O LEU B 141 N LEU B 216
SHEET 7 BB 7 VAL B 171 LEU B 174 1 O ARG B 172 N VAL B 142
SHEET 1 BC 4 VAL B 359 ARG B 365 0
SHEET 2 BC 4 PHE B 368 ILE B 373 -1 O PHE B 368 N ARG B 365
SHEET 3 BC 4 VAL B 410 MET B 413 -1 O LEU B 411 N ILE B 371
SHEET 4 BC 4 SER B 402 VAL B 404 -1 O SER B 402 N LYS B 412
LINK O ALA A 353 NA NA A1443 1555 1555 2.32
LINK O SER A 356 NA NA A1443 1555 1555 2.23
LINK O VAL A 359 NA NA A1443 1555 1555 2.24
LINK NA NA A1443 O HOH A2285 1555 1555 2.24
SITE 1 AC1 19 ARG A 90 THR A 311 HOH A2115 HOH A2121
SITE 2 AC1 19 HOH A2263 TYR B 61 GLY B 120 SER B 121
SITE 3 AC1 19 ASN B 124 TYR B 147 HIS B 148 ASP B 251
SITE 4 AC1 19 GLN B 254 LYS B 281 LYS B 412 ARG B 414
SITE 5 AC1 19 HOH B2015 HOH B2049 HOH B2073
SITE 1 AC2 20 TYR A 61 GLY A 120 SER A 121 ASN A 124
SITE 2 AC2 20 TYR A 147 HIS A 148 ASP A 251 GLN A 254
SITE 3 AC2 20 LYS A 281 LYS A 412 ARG A 414 HOH A2041
SITE 4 AC2 20 HOH A2044 HOH A2117 HOH A2118 HOH A2151
SITE 5 AC2 20 HOH A2152 HOH A2308 ARG B 90 THR B 311
SITE 1 AC3 3 GLY A 232 GLU A 235 ASN A 271
SITE 1 AC4 3 GLY B 232 GLU B 235 ASN B 271
SITE 1 AC5 4 ALA A 353 SER A 356 VAL A 359 HOH A2285
CRYST1 76.166 96.371 121.897 90.00 90.00 90.00 P 21 21 21 16
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 0.013129 0.000000 0.000000 0.00000
SCALE2 0.000000 0.010377 0.000000 0.00000
SCALE3 0.000000 0.000000 0.008204 0.00000
MTRIX1 1 0.230400 -0.473900 0.849900 26.18000
MTRIX2 1 -0.470400 -0.818800 -0.329000 -11.26000
MTRIX3 1 0.851900 -0.324000 -0.411600 -44.20000