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 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 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