HEADER HYDROLASE 16-JUN-10 3NIY
TITLE CRYSTAL STRUCTURE OF NATIVE XYLANASE 10B FROM THERMOTOGA PETROPHILA
TITLE 2 RKU-1
COMPND MOL_ID: 1;
COMPND 2 MOLECULE: ENDO-1,4-BETA-XYLANASE;
COMPND 3 CHAIN: A, B;
COMPND 4 FRAGMENT: UNP RESIDUES 21 TO 344;
COMPND 5 EC: 3.2.1.8;
COMPND 6 ENGINEERED: YES
SOURCE MOL_ID: 1;
SOURCE 2 ORGANISM_SCIENTIFIC: THERMOTOGA PETROPHILA RKU-1;
SOURCE 3 ORGANISM_TAXID: 390874;
SOURCE 4 STRAIN: RKU-1;
SOURCE 5 GENE: TPET_0854;
SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI;
SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562
KEYWDS TIM-BARREL, XYLANASE, HYDROLASE
EXPDTA X-RAY DIFFRACTION
AUTHOR C.R.SANTOS,A.N.MEZA,D.M.TRINDADE,R.RULLER,F.M.SQUINA,R.A.PRADE,
AUTHOR 2 M.T.MURAKAMI
REVDAT 3 21-FEB-24 3NIY 1 REMARK SEQADV
REVDAT 2 08-NOV-17 3NIY 1 REMARK
REVDAT 1 04-MAY-11 3NIY 0
JRNL AUTH C.R.SANTOS,A.N.MEZA,Z.B.HOFFMAM,J.C.SILVA,T.M.ALVAREZ,
JRNL AUTH 2 R.RULLER,G.M.GIESEL,H.VERLI,F.M.SQUINA,R.A.PRADE,
JRNL AUTH 3 M.T.MURAKAMI
JRNL TITL THERMAL-INDUCED CONFORMATIONAL CHANGES IN THE PRODUCT
JRNL TITL 2 RELEASE AREA DRIVE THE ENZYMATIC ACTIVITY OF XYLANASES 10B:
JRNL TITL 3 CRYSTAL STRUCTURE, CONFORMATIONAL STABILITY AND FUNCTIONAL
JRNL TITL 4 CHARACTERIZATION OF THE XYLANASE 10B FROM THERMOTOGA
JRNL TITL 5 PETROPHILA RKU-1.
JRNL REF BIOCHEM.BIOPHYS.RES.COMMUN. V. 403 214 2010
JRNL REFN ISSN 0006-291X
JRNL PMID 21070746
JRNL DOI 10.1016/J.BBRC.2010.11.010
REMARK 2
REMARK 2 RESOLUTION. 1.58 ANGSTROMS.
REMARK 3
REMARK 3 REFINEMENT.
REMARK 3 PROGRAM : REFMAC 5.5.0102
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) : 1.58
REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 31.24
REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL
REMARK 3 COMPLETENESS FOR RANGE (%) : 92.5
REMARK 3 NUMBER OF REFLECTIONS : 87311
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) : 0.160
REMARK 3 R VALUE (WORKING SET) : 0.158
REMARK 3 FREE R VALUE : 0.196
REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.000
REMARK 3 FREE R VALUE TEST SET COUNT : 4584
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) : 1.58
REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.62
REMARK 3 REFLECTION IN BIN (WORKING SET) : 5793
REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 82.99
REMARK 3 BIN R VALUE (WORKING SET) : 0.2920
REMARK 3 BIN FREE R VALUE SET COUNT : 282
REMARK 3 BIN FREE R VALUE : 0.3580
REMARK 3
REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT.
REMARK 3 PROTEIN ATOMS : 5440
REMARK 3 NUCLEIC ACID ATOMS : 0
REMARK 3 HETEROGEN ATOMS : 45
REMARK 3 SOLVENT ATOMS : 616
REMARK 3
REMARK 3 B VALUES.
REMARK 3 FROM WILSON PLOT (A**2) : NULL
REMARK 3 MEAN B VALUE (OVERALL, A**2) : 16.64
REMARK 3 OVERALL ANISOTROPIC B VALUE.
REMARK 3 B11 (A**2) : -0.37000
REMARK 3 B22 (A**2) : 0.18000
REMARK 3 B33 (A**2) : 0.35000
REMARK 3 B12 (A**2) : -0.01000
REMARK 3 B13 (A**2) : -0.09000
REMARK 3 B23 (A**2) : -0.47000
REMARK 3
REMARK 3 ESTIMATED OVERALL COORDINATE ERROR.
REMARK 3 ESU BASED ON R VALUE (A): NULL
REMARK 3 ESU BASED ON FREE R VALUE (A): 0.085
REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.048
REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 1.325
REMARK 3
REMARK 3 CORRELATION COEFFICIENTS.
REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.968
REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.951
REMARK 3
REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT
REMARK 3 BOND LENGTHS REFINED ATOMS (A): 5638 ; 0.030 ; 0.022
REMARK 3 BOND LENGTHS OTHERS (A): NULL ; NULL ; NULL
REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 7630 ; 2.415 ; 1.941
REMARK 3 BOND ANGLES OTHERS (DEGREES): NULL ; NULL ; NULL
REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 649 ; 6.279 ; 5.000
REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 298 ;31.943 ;24.463
REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 986 ;13.328 ;15.000
REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 28 ;20.297 ;15.000
REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 780 ; 0.187 ; 0.200
REMARK 3 GENERAL PLANES REFINED ATOMS (A): 4348 ; 0.014 ; 0.021
REMARK 3 GENERAL PLANES OTHERS (A): NULL ; NULL ; NULL
REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): NULL ; NULL ; NULL
REMARK 3 NON-BONDED CONTACTS OTHERS (A): NULL ; NULL ; NULL
REMARK 3 NON-BONDED TORSION REFINED ATOMS (A): NULL ; NULL ; NULL
REMARK 3 NON-BONDED TORSION OTHERS (A): NULL ; NULL ; NULL
REMARK 3 H-BOND (X...Y) REFINED ATOMS (A): NULL ; NULL ; NULL
REMARK 3 H-BOND (X...Y) OTHERS (A): NULL ; NULL ; NULL
REMARK 3 POTENTIAL METAL-ION REFINED ATOMS (A): NULL ; NULL ; NULL
REMARK 3 POTENTIAL METAL-ION OTHERS (A): NULL ; NULL ; NULL
REMARK 3 SYMMETRY VDW REFINED ATOMS (A): NULL ; NULL ; NULL
REMARK 3 SYMMETRY VDW OTHERS (A): NULL ; NULL ; NULL
REMARK 3 SYMMETRY H-BOND REFINED ATOMS (A): NULL ; NULL ; NULL
REMARK 3 SYMMETRY H-BOND OTHERS (A): NULL ; NULL ; NULL
REMARK 3 SYMMETRY METAL-ION REFINED ATOMS (A): NULL ; NULL ; NULL
REMARK 3 SYMMETRY METAL-ION OTHERS (A): NULL ; NULL ; NULL
REMARK 3
REMARK 3 ISOTROPIC THERMAL FACTOR RESTRAINTS. COUNT RMS WEIGHT
REMARK 3 MAIN-CHAIN BOND REFINED ATOMS (A**2): 3261 ; 1.518 ; 1.500
REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL
REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 5275 ; 2.463 ; 2.000
REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL
REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 2377 ; 3.865 ; 3.000
REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL
REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 2355 ; 6.160 ; 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 : NULL
REMARK 3
REMARK 3 BULK SOLVENT MODELLING.
REMARK 3 METHOD USED : MASK
REMARK 3 PARAMETERS FOR MASK CALCULATION
REMARK 3 VDW PROBE RADIUS : 1.40
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 3NIY COMPLIES WITH FORMAT V. 3.30, 13-JUL-11
REMARK 100
REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 23-JUN-10.
REMARK 100 THE DEPOSITION ID IS D_1000059887.
REMARK 200
REMARK 200 EXPERIMENTAL DETAILS
REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION
REMARK 200 DATE OF DATA COLLECTION : 03-MAY-10
REMARK 200 TEMPERATURE (KELVIN) : 100
REMARK 200 PH : 4.3
REMARK 200 NUMBER OF CRYSTALS USED : 1
REMARK 200
REMARK 200 SYNCHROTRON (Y/N) : Y
REMARK 200 RADIATION SOURCE : LNLS
REMARK 200 BEAMLINE : W01B-MX2
REMARK 200 X-RAY GENERATOR MODEL : NULL
REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M
REMARK 200 WAVELENGTH OR RANGE (A) : 1.458
REMARK 200 MONOCHROMATOR : SILICON DOUBLE-CRYSTAL
REMARK 200 OPTICS : NULL
REMARK 200
REMARK 200 DETECTOR TYPE : CCD
REMARK 200 DETECTOR MANUFACTURER : MARMOSAIC 225 MM CCD
REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000
REMARK 200 DATA SCALING SOFTWARE : HKL-2000
REMARK 200
REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 91930
REMARK 200 RESOLUTION RANGE HIGH (A) : 1.580
REMARK 200 RESOLUTION RANGE LOW (A) : 31.240
REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 3.000
REMARK 200
REMARK 200 OVERALL.
REMARK 200 COMPLETENESS FOR RANGE (%) : 92.8
REMARK 200 DATA REDUNDANCY : NULL
REMARK 200 R MERGE (I) : 0.10100
REMARK 200 R SYM (I) : NULL
REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : NULL
REMARK 200
REMARK 200 IN THE HIGHEST RESOLUTION SHELL.
REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.58
REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.64
REMARK 200 COMPLETENESS FOR SHELL (%) : 86.8
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: MOLREP
REMARK 200 STARTING MODEL: NULL
REMARK 200
REMARK 200 REMARK: NULL
REMARK 280
REMARK 280 CRYSTAL
REMARK 280 SOLVENT CONTENT, VS (%): 46.50
REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.30
REMARK 280
REMARK 280 CRYSTALLIZATION CONDITIONS: PEG8000 GLYCEROL SODIUM ACETATE LITIUM
REMARK 280 SULFATE, PH 4.3, VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 291K
REMARK 290
REMARK 290 CRYSTALLOGRAPHIC SYMMETRY
REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 1
REMARK 290
REMARK 290 SYMOP SYMMETRY
REMARK 290 NNNMMM OPERATOR
REMARK 290 1555 X,Y,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
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: MONOMERIC
REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: MONOMERIC
REMARK 350 SOFTWARE USED: PISA
REMARK 350 APPLY THE FOLLOWING TO CHAINS: A
REMARK 350 BIOMT1 1 1.000000 0.000000 0.000000 0.00000
REMARK 350 BIOMT2 1 0.000000 1.000000 0.000000 0.00000
REMARK 350 BIOMT3 1 0.000000 0.000000 1.000000 0.00000
REMARK 350
REMARK 350 BIOMOLECULE: 2
REMARK 350 AUTHOR DETERMINED BIOLOGICAL UNIT: MONOMERIC
REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: MONOMERIC
REMARK 350 SOFTWARE USED: PISA
REMARK 350 APPLY THE FOLLOWING TO CHAINS: 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 GLY A 2
REMARK 465 HIS A 3
REMARK 465 HIS A 4
REMARK 465 HIS A 5
REMARK 465 HIS A 6
REMARK 465 HIS A 7
REMARK 465 HIS A 8
REMARK 465 GLU A 9
REMARK 465 ASN A 10
REMARK 465 LEU A 11
REMARK 465 TYR A 12
REMARK 465 PHE A 13
REMARK 465 GLN A 14
REMARK 465 GLY A 15
REMARK 465 MET B 1
REMARK 465 GLY B 2
REMARK 465 HIS B 3
REMARK 465 HIS B 4
REMARK 465 HIS B 5
REMARK 465 HIS B 6
REMARK 465 HIS B 7
REMARK 465 HIS B 8
REMARK 465 GLU B 9
REMARK 465 ASN B 10
REMARK 465 LEU B 11
REMARK 465 TYR B 12
REMARK 465 PHE B 13
REMARK 465 GLN B 14
REMARK 465 GLY B 15
REMARK 465 HIS B 16
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 ASP B 154 O HOH B 459 1.83
REMARK 500 NE2 GLN B 108 O HOH B 437 1.89
REMARK 500 O HOH A 621 O HOH B 597 2.00
REMARK 500 O HOH A 429 O HOH A 535 2.00
REMARK 500 O HOH B 442 O HOH B 577 2.05
REMARK 500 OD2 ASP B 183 O HOH B 546 2.06
REMARK 500 O HOH B 446 O HOH B 546 2.09
REMARK 500 O HOH A 621 O HOH B 559 2.10
REMARK 500 O HOH B 577 O HOH B 586 2.13
REMARK 500 O HOH A 425 O HOH A 453 2.13
REMARK 500 OE2 GLU B 27 O HOH B 643 2.15
REMARK 500 O HOH A 509 O HOH A 522 2.16
REMARK 500 OE1 GLU A 27 O HOH A 419 2.17
REMARK 500 O HOH A 487 O HOH A 646 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 O HOH B 550 O HOH B 616 1455 2.11
REMARK 500 O2 SO4 A 345 O HOH B 629 1544 2.12
REMARK 500 O HOH A 538 O HOH A 650 1655 2.18
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 TYR A 50 CD1 TYR A 50 CE1 0.108
REMARK 500 TRP A 69 CB TRP A 69 CG -0.152
REMARK 500 ARG A 239 CG ARG A 239 CD 0.167
REMARK 500 GLU B 27 CG GLU B 27 CD 0.100
REMARK 500 TRP B 69 CB TRP B 69 CG -0.141
REMARK 500 GLU B 75 CB GLU B 75 CG -0.189
REMARK 500 GLU B 75 CG GLU B 75 CD -0.160
REMARK 500 LYS B 86 CD LYS B 86 CE 0.158
REMARK 500 LYS B 215 CB LYS B 215 CG -0.245
REMARK 500 ARG B 240 CG ARG B 240 CD 0.160
REMARK 500 GLU B 334 CG GLU B 334 CD 0.133
REMARK 500 GLU B 334 CD GLU B 334 OE2 0.085
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 PHE A 35 CB - CG - CD2 ANGL. DEV. = -4.2 DEGREES
REMARK 500 TYR A 50 CD1 - CE1 - CZ ANGL. DEV. = -6.2 DEGREES
REMARK 500 ARG A 116 NE - CZ - NH1 ANGL. DEV. = -4.0 DEGREES
REMARK 500 ARG A 177 NE - CZ - NH2 ANGL. DEV. = -3.6 DEGREES
REMARK 500 ARG A 239 CG - CD - NE ANGL. DEV. = 13.8 DEGREES
REMARK 500 ARG A 244 NE - CZ - NH2 ANGL. DEV. = -3.5 DEGREES
REMARK 500 ARG B 23 NE - CZ - NH2 ANGL. DEV. = -3.6 DEGREES
REMARK 500 MET B 51 CG - SD - CE ANGL. DEV. = -13.9 DEGREES
REMARK 500 ARG B 116 NE - CZ - NH2 ANGL. DEV. = -4.1 DEGREES
REMARK 500 PHE B 138 CB - CG - CD2 ANGL. DEV. = -4.6 DEGREES
REMARK 500 LYS B 215 CB - CG - CD ANGL. DEV. = -16.4 DEGREES
REMARK 500 ARG B 244 NE - CZ - NH2 ANGL. DEV. = -4.0 DEGREES
REMARK 500 GLU B 334 CG - CD - OE2 ANGL. DEV. = 13.7 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 65 -19.24 -140.83
REMARK 500 GLU A 256 43.53 -143.93
REMARK 500 SER A 266 59.22 29.56
REMARK 500 PHE A 299 -22.57 -144.05
REMARK 500 ASN B 65 -17.87 -140.57
REMARK 500 GLU B 256 48.56 -141.62
REMARK 500 PHE B 299 -20.99 -146.46
REMARK 500 LEU B 317 -169.75 -118.84
REMARK 500
REMARK 500 REMARK: NULL
REMARK 800
REMARK 800 SITE
REMARK 800 SITE_IDENTIFIER: AC1
REMARK 800 EVIDENCE_CODE: SOFTWARE
REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SO4 A 342
REMARK 800
REMARK 800 SITE_IDENTIFIER: AC2
REMARK 800 EVIDENCE_CODE: SOFTWARE
REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SO4 A 343
REMARK 800
REMARK 800 SITE_IDENTIFIER: AC3
REMARK 800 EVIDENCE_CODE: SOFTWARE
REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SO4 A 344
REMARK 800
REMARK 800 SITE_IDENTIFIER: AC4
REMARK 800 EVIDENCE_CODE: SOFTWARE
REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SO4 A 345
REMARK 800
REMARK 800 SITE_IDENTIFIER: AC5
REMARK 800 EVIDENCE_CODE: SOFTWARE
REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ACT A 346
REMARK 800
REMARK 800 SITE_IDENTIFIER: AC6
REMARK 800 EVIDENCE_CODE: SOFTWARE
REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ACT A 347
REMARK 800
REMARK 800 SITE_IDENTIFIER: AC7
REMARK 800 EVIDENCE_CODE: SOFTWARE
REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ACT A 348
REMARK 800
REMARK 800 SITE_IDENTIFIER: AC8
REMARK 800 EVIDENCE_CODE: SOFTWARE
REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SO4 B 342
REMARK 800
REMARK 800 SITE_IDENTIFIER: AC9
REMARK 800 EVIDENCE_CODE: SOFTWARE
REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ACT B 343
REMARK 800
REMARK 800 SITE_IDENTIFIER: BC1
REMARK 800 EVIDENCE_CODE: SOFTWARE
REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ACT B 344
REMARK 900
REMARK 900 RELATED ENTRIES
REMARK 900 RELATED ID: 3NJ3 RELATED DB: PDB
DBREF 3NIY A 18 341 UNP A5IL00 A5IL00_THEP1 21 344
DBREF 3NIY B 18 341 UNP A5IL00 A5IL00_THEP1 21 344
SEQADV 3NIY MET A 1 UNP A5IL00 EXPRESSION TAG
SEQADV 3NIY GLY A 2 UNP A5IL00 EXPRESSION TAG
SEQADV 3NIY HIS A 3 UNP A5IL00 EXPRESSION TAG
SEQADV 3NIY HIS A 4 UNP A5IL00 EXPRESSION TAG
SEQADV 3NIY HIS A 5 UNP A5IL00 EXPRESSION TAG
SEQADV 3NIY HIS A 6 UNP A5IL00 EXPRESSION TAG
SEQADV 3NIY HIS A 7 UNP A5IL00 EXPRESSION TAG
SEQADV 3NIY HIS A 8 UNP A5IL00 EXPRESSION TAG
SEQADV 3NIY GLU A 9 UNP A5IL00 EXPRESSION TAG
SEQADV 3NIY ASN A 10 UNP A5IL00 EXPRESSION TAG
SEQADV 3NIY LEU A 11 UNP A5IL00 EXPRESSION TAG
SEQADV 3NIY TYR A 12 UNP A5IL00 EXPRESSION TAG
SEQADV 3NIY PHE A 13 UNP A5IL00 EXPRESSION TAG
SEQADV 3NIY GLN A 14 UNP A5IL00 EXPRESSION TAG
SEQADV 3NIY GLY A 15 UNP A5IL00 EXPRESSION TAG
SEQADV 3NIY HIS A 16 UNP A5IL00 EXPRESSION TAG
SEQADV 3NIY MET A 17 UNP A5IL00 EXPRESSION TAG
SEQADV 3NIY MET B 1 UNP A5IL00 EXPRESSION TAG
SEQADV 3NIY GLY B 2 UNP A5IL00 EXPRESSION TAG
SEQADV 3NIY HIS B 3 UNP A5IL00 EXPRESSION TAG
SEQADV 3NIY HIS B 4 UNP A5IL00 EXPRESSION TAG
SEQADV 3NIY HIS B 5 UNP A5IL00 EXPRESSION TAG
SEQADV 3NIY HIS B 6 UNP A5IL00 EXPRESSION TAG
SEQADV 3NIY HIS B 7 UNP A5IL00 EXPRESSION TAG
SEQADV 3NIY HIS B 8 UNP A5IL00 EXPRESSION TAG
SEQADV 3NIY GLU B 9 UNP A5IL00 EXPRESSION TAG
SEQADV 3NIY ASN B 10 UNP A5IL00 EXPRESSION TAG
SEQADV 3NIY LEU B 11 UNP A5IL00 EXPRESSION TAG
SEQADV 3NIY TYR B 12 UNP A5IL00 EXPRESSION TAG
SEQADV 3NIY PHE B 13 UNP A5IL00 EXPRESSION TAG
SEQADV 3NIY GLN B 14 UNP A5IL00 EXPRESSION TAG
SEQADV 3NIY GLY B 15 UNP A5IL00 EXPRESSION TAG
SEQADV 3NIY HIS B 16 UNP A5IL00 EXPRESSION TAG
SEQADV 3NIY MET B 17 UNP A5IL00 EXPRESSION TAG
SEQRES 1 A 341 MET GLY HIS HIS HIS HIS HIS HIS GLU ASN LEU TYR PHE
SEQRES 2 A 341 GLN GLY HIS MET GLN ASN VAL SER LEU ARG GLU LEU ALA
SEQRES 3 A 341 GLU LYS LEU ASN ILE TYR ILE GLY PHE ALA ALA ILE ASN
SEQRES 4 A 341 ASN PHE TRP SER LEU SER ASP GLU GLU LYS TYR MET GLU
SEQRES 5 A 341 VAL ALA ARG ARG GLU PHE ASN ILE LEU THR PRO GLU ASN
SEQRES 6 A 341 GLN MET LYS TRP ASP THR ILE HIS PRO GLU ARG ASP ARG
SEQRES 7 A 341 TYR ASN PHE THR PRO ALA GLU LYS HIS VAL GLU PHE ALA
SEQRES 8 A 341 GLU GLU ASN ASN MET ILE VAL HIS GLY HIS THR LEU VAL
SEQRES 9 A 341 TRP HIS ASN GLN LEU PRO GLY TRP ILE THR GLY ARG GLU
SEQRES 10 A 341 TRP THR LYS GLU GLU LEU LEU ASN VAL LEU GLU ASP HIS
SEQRES 11 A 341 ILE LYS THR VAL VAL SER HIS PHE LYS GLY ARG VAL LYS
SEQRES 12 A 341 ILE TRP ASP VAL VAL ASN GLU ALA VAL SER ASP SER GLY
SEQRES 13 A 341 THR TYR ARG GLU SER VAL TRP TYR LYS THR ILE GLY PRO
SEQRES 14 A 341 GLU TYR ILE GLU LYS ALA PHE ARG TRP THR LYS GLU ALA
SEQRES 15 A 341 ASP PRO ASP ALA ILE LEU ILE TYR ASN ASP TYR SER ILE
SEQRES 16 A 341 GLU GLU ILE ASN ALA LYS SER ASN PHE VAL TYR ASN MET
SEQRES 17 A 341 ILE LYS GLU LEU LYS GLU LYS GLY VAL PRO VAL ASP GLY
SEQRES 18 A 341 ILE GLY PHE GLN MET HIS ILE ASP TYR ARG GLY LEU ASN
SEQRES 19 A 341 TYR ASP SER PHE ARG ARG ASN LEU GLU ARG PHE ALA LYS
SEQRES 20 A 341 LEU GLY LEU GLN ILE TYR ILE THR GLU MET ASP VAL ARG
SEQRES 21 A 341 ILE PRO LEU SER GLY SER GLU ASP TYR TYR LEU LYS LYS
SEQRES 22 A 341 GLN ALA GLU ILE CYS ALA LYS ILE PHE ASP ILE CYS LEU
SEQRES 23 A 341 ASP ASN PRO ALA VAL LYS ALA ILE GLN PHE TRP GLY PHE
SEQRES 24 A 341 THR ASP LYS TYR SER TRP VAL PRO GLY PHE PHE LYS GLY
SEQRES 25 A 341 TYR GLY LYS ALA LEU LEU PHE ASP GLU ASN TYR ASN PRO
SEQRES 26 A 341 LYS PRO CYS TYR TYR ALA ILE LYS GLU VAL LEU GLU LYS
SEQRES 27 A 341 LYS ILE GLU
SEQRES 1 B 341 MET GLY HIS HIS HIS HIS HIS HIS GLU ASN LEU TYR PHE
SEQRES 2 B 341 GLN GLY HIS MET GLN ASN VAL SER LEU ARG GLU LEU ALA
SEQRES 3 B 341 GLU LYS LEU ASN ILE TYR ILE GLY PHE ALA ALA ILE ASN
SEQRES 4 B 341 ASN PHE TRP SER LEU SER ASP GLU GLU LYS TYR MET GLU
SEQRES 5 B 341 VAL ALA ARG ARG GLU PHE ASN ILE LEU THR PRO GLU ASN
SEQRES 6 B 341 GLN MET LYS TRP ASP THR ILE HIS PRO GLU ARG ASP ARG
SEQRES 7 B 341 TYR ASN PHE THR PRO ALA GLU LYS HIS VAL GLU PHE ALA
SEQRES 8 B 341 GLU GLU ASN ASN MET ILE VAL HIS GLY HIS THR LEU VAL
SEQRES 9 B 341 TRP HIS ASN GLN LEU PRO GLY TRP ILE THR GLY ARG GLU
SEQRES 10 B 341 TRP THR LYS GLU GLU LEU LEU ASN VAL LEU GLU ASP HIS
SEQRES 11 B 341 ILE LYS THR VAL VAL SER HIS PHE LYS GLY ARG VAL LYS
SEQRES 12 B 341 ILE TRP ASP VAL VAL ASN GLU ALA VAL SER ASP SER GLY
SEQRES 13 B 341 THR TYR ARG GLU SER VAL TRP TYR LYS THR ILE GLY PRO
SEQRES 14 B 341 GLU TYR ILE GLU LYS ALA PHE ARG TRP THR LYS GLU ALA
SEQRES 15 B 341 ASP PRO ASP ALA ILE LEU ILE TYR ASN ASP TYR SER ILE
SEQRES 16 B 341 GLU GLU ILE ASN ALA LYS SER ASN PHE VAL TYR ASN MET
SEQRES 17 B 341 ILE LYS GLU LEU LYS GLU LYS GLY VAL PRO VAL ASP GLY
SEQRES 18 B 341 ILE GLY PHE GLN MET HIS ILE ASP TYR ARG GLY LEU ASN
SEQRES 19 B 341 TYR ASP SER PHE ARG ARG ASN LEU GLU ARG PHE ALA LYS
SEQRES 20 B 341 LEU GLY LEU GLN ILE TYR ILE THR GLU MET ASP VAL ARG
SEQRES 21 B 341 ILE PRO LEU SER GLY SER GLU ASP TYR TYR LEU LYS LYS
SEQRES 22 B 341 GLN ALA GLU ILE CYS ALA LYS ILE PHE ASP ILE CYS LEU
SEQRES 23 B 341 ASP ASN PRO ALA VAL LYS ALA ILE GLN PHE TRP GLY PHE
SEQRES 24 B 341 THR ASP LYS TYR SER TRP VAL PRO GLY PHE PHE LYS GLY
SEQRES 25 B 341 TYR GLY LYS ALA LEU LEU PHE ASP GLU ASN TYR ASN PRO
SEQRES 26 B 341 LYS PRO CYS TYR TYR ALA ILE LYS GLU VAL LEU GLU LYS
SEQRES 27 B 341 LYS ILE GLU
HET SO4 A 342 5
HET SO4 A 343 5
HET SO4 A 344 5
HET SO4 A 345 5
HET ACT A 346 4
HET ACT A 347 4
HET ACT A 348 4
HET SO4 B 342 5
HET ACT B 343 4
HET ACT B 344 4
HETNAM SO4 SULFATE ION
HETNAM ACT ACETATE ION
FORMUL 3 SO4 5(O4 S 2-)
FORMUL 7 ACT 5(C2 H3 O2 1-)
FORMUL 13 HOH *616(H2 O)
HELIX 1 1 SER A 21 LEU A 29 1 9
HELIX 2 2 ASN A 40 LEU A 44 5 5
HELIX 3 3 ASP A 46 PHE A 58 1 13
HELIX 4 4 LYS A 68 HIS A 73 1 6
HELIX 5 5 PHE A 81 ASN A 94 1 14
HELIX 6 6 PRO A 110 GLY A 115 1 6
HELIX 7 7 THR A 119 PHE A 138 1 20
HELIX 8 8 SER A 161 GLY A 168 1 8
HELIX 9 9 PRO A 169 ASP A 183 1 15
HELIX 10 10 ASN A 199 LYS A 215 1 17
HELIX 11 11 ASN A 234 LEU A 248 1 15
HELIX 12 12 SER A 266 ASP A 287 1 22
HELIX 13 13 TRP A 305 PHE A 310 1 6
HELIX 14 14 LYS A 326 GLU A 341 1 16
HELIX 15 15 SER B 21 LEU B 29 1 9
HELIX 16 16 ASN B 40 LEU B 44 5 5
HELIX 17 17 ASP B 46 PHE B 58 1 13
HELIX 18 18 LYS B 68 HIS B 73 1 6
HELIX 19 19 PHE B 81 ASN B 94 1 14
HELIX 20 20 PRO B 110 GLY B 115 1 6
HELIX 21 21 THR B 119 PHE B 138 1 20
HELIX 22 22 SER B 161 GLY B 168 1 8
HELIX 23 23 PRO B 169 ASP B 183 1 15
HELIX 24 24 ASN B 199 LYS B 215 1 17
HELIX 25 25 ASN B 234 LEU B 248 1 15
HELIX 26 26 SER B 266 ASP B 287 1 22
HELIX 27 27 TRP B 305 PHE B 310 1 6
HELIX 28 28 LYS B 326 GLU B 341 1 16
SHEET 1 A11 HIS A 227 ASP A 229 0
SHEET 2 A11 TYR A 313 GLY A 314 0
SHEET 3 A11 GLY A 221 PHE A 224 0
SHEET 4 A11 ILE A 187 ASP A 192 1 N TYR A 190 O GLY A 223
SHEET 5 A11 ILE A 144 ASN A 149 1 N TRP A 145 O ILE A 189
SHEET 6 A11 ILE A 97 VAL A 104 1 N GLY A 100 O ILE A 144
SHEET 7 A11 ILE A 60 PRO A 63 1 N LEU A 61 O HIS A 99
SHEET 8 A11 TYR A 32 ALA A 37 1 N ALA A 37 O THR A 62
SHEET 9 A11 VAL A 291 PHE A 296 1 O PHE A 296 N GLY A 34
SHEET 10 A11 GLN A 251 PRO A 262 1 N ILE A 254 O GLN A 295
SHEET 11 A11 TYR A 313 GLY A 314 -1 O GLY A 314 N ILE A 261
SHEET 1 B 2 ARG A 78 ASN A 80 0
SHEET 2 B 2 ARG B 78 ASN B 80 -1 O TYR B 79 N TYR A 79
SHEET 1 C11 HIS B 227 ASP B 229 0
SHEET 2 C11 TYR B 313 GLY B 314 0
SHEET 3 C11 GLY B 221 PHE B 224 0
SHEET 4 C11 ILE B 187 ASP B 192 1 N TYR B 190 O GLY B 223
SHEET 5 C11 ILE B 144 ASN B 149 1 N TRP B 145 O ILE B 189
SHEET 6 C11 ILE B 97 VAL B 104 1 N GLY B 100 O ILE B 144
SHEET 7 C11 ILE B 60 PRO B 63 1 N LEU B 61 O HIS B 99
SHEET 8 C11 TYR B 32 ALA B 37 1 N ALA B 37 O THR B 62
SHEET 9 C11 VAL B 291 PHE B 296 1 O ILE B 294 N TYR B 32
SHEET 10 C11 GLN B 251 PRO B 262 1 N ILE B 252 O LYS B 292
SHEET 11 C11 TYR B 313 GLY B 314 -1 O GLY B 314 N ILE B 261
CISPEP 1 HIS A 101 THR A 102 0 -10.26
CISPEP 2 HIS B 101 THR B 102 0 -7.60
SITE 1 AC1 6 PRO A 110 GLY A 111 HOH A 430 HOH A 552
SITE 2 AC1 6 HOH A 604 LYS B 247
SITE 1 AC2 4 ACT A 347 HOH A 607 ARG B 239 LYS B 280
SITE 1 AC3 6 ARG A 78 HOH A 600 PRO B 74 ARG B 78
SITE 2 AC3 6 ASN B 80 HOH B 395
SITE 1 AC4 4 ARG A 239 LYS A 280 ACT B 343 HOH B 629
SITE 1 AC5 4 GLU A 64 SER A 304 TRP A 305 HOH A 361
SITE 1 AC6 5 ASN A 199 ALA A 200 SO4 A 343 HOH A 383
SITE 2 AC6 5 HOH B 382
SITE 1 AC7 5 TYR A 193 HIS A 227 HOH A 403 HOH A 433
SITE 2 AC7 5 HOH A 534
SITE 1 AC8 3 LYS A 215 SER B 45 LYS B 302
SITE 1 AC9 5 SO4 A 345 HOH A 357 ASN B 199 ALA B 200
SITE 2 AC9 5 HOH B 373
SITE 1 BC1 3 HIS B 227 HOH B 599 HOH B 636
CRYST1 58.538 58.554 61.579 84.54 70.82 68.87 P 1 2
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 0.017083 -0.006602 -0.006118 0.00000
SCALE2 0.000000 0.018309 0.000484 0.00000
SCALE3 0.000000 0.000000 0.017200 0.00000
(ATOM LINES ARE NOT SHOWN.)
END
