HEADER BIOSYNTHETIC PROTEIN 09-JUL-19 6KG1 TITLE NIFS FROM HELICOBACTER PYLORI, SOAKED WITH L-CYSTEINE FOR 180 SEC COMPND MOL_ID: 1; COMPND 2 MOLECULE: CYSTEINE DESULFURASE ISCS; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: NIFS; COMPND 5 EC: 2.8.1.7; COMPND 6 ENGINEERED: YES; COMPND 7 MUTATION: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: HELICOBACTER PYLORI (STRAIN ATCC 700392 / SOURCE 3 26695); SOURCE 4 ORGANISM_TAXID: 85962; SOURCE 5 STRAIN: ATCC 700392 / 26695; SOURCE 6 GENE: ISCS, HP_0220; SOURCE 7 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21(DE3); SOURCE 8 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 9 EXPRESSION_SYSTEM_VARIANT: C41 KEYWDS IRON, SULFUR, CYSTEINE DESULFURASE, REACTION INTERMEDIATE, KEYWDS 2 BIOSYNTHETIC PROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR R.NAKAMURA,Y.TAKAHASHI,T.FUJISHIRO REVDAT 4 22-NOV-23 6KG1 1 REMARK REVDAT 3 01-APR-20 6KG1 1 JRNL REVDAT 2 23-OCT-19 6KG1 1 JRNL REVDAT 1 16-OCT-19 6KG1 0 JRNL AUTH R.NAKAMURA,M.HIKITA,S.OGAWA,Y.TAKAHASHI,T.FUJISHIRO JRNL TITL SNAPSHOTS OF PLP-SUBSTRATE AND PLP-PRODUCT EXTERNAL JRNL TITL 2 ALDIMINES AS INTERMEDIATES IN TWO TYPES OF CYSTEINE JRNL TITL 3 DESULFURASE ENZYMES. JRNL REF FEBS J. V. 287 1138 2020 JRNL REFN ISSN 1742-464X JRNL PMID 31587510 JRNL DOI 10.1111/FEBS.15081 REMARK 2 REMARK 2 RESOLUTION. 2.70 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.8.0253 REMARK 3 AUTHORS : MURSHUDOV,SKUBAK,LEBEDEV,PANNU,STEINER, REMARK 3 : NICHOLLS,WINN,LONG,VAGIN REMARK 3 REMARK 3 REFINEMENT TARGET : NULL REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.70 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 49.18 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 100.0 REMARK 3 NUMBER OF REFLECTIONS : 19253 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) : 0.183 REMARK 3 R VALUE (WORKING SET) : 0.180 REMARK 3 FREE R VALUE : 0.231 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.000 REMARK 3 FREE R VALUE TEST SET COUNT : 1014 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) : 2.70 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.77 REMARK 3 REFLECTION IN BIN (WORKING SET) : 1389 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 100.0 REMARK 3 BIN R VALUE (WORKING SET) : 0.3260 REMARK 3 BIN FREE R VALUE SET COUNT : 73 REMARK 3 BIN FREE R VALUE : 0.3930 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 2780 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 26 REMARK 3 SOLVENT ATOMS : 8 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 73.22 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 92.07 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 0.23000 REMARK 3 B22 (A**2) : 0.23000 REMARK 3 B33 (A**2) : -0.46000 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): 0.294 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.243 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.205 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 22.207 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.961 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.934 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 2854 ; 0.015 ; 0.012 REMARK 3 BOND LENGTHS OTHERS (A): NULL ; NULL ; NULL REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 3866 ; 2.926 ; 1.641 REMARK 3 BOND ANGLES OTHERS (DEGREES): NULL ; NULL ; NULL REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 357 ; 8.438 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 142 ;38.505 ;22.394 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 495 ;21.917 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 18 ;19.989 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 384 ; 0.226 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 2138 ; 0.015 ; 0.020 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): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): NULL ; NULL ; NULL 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 : 3 REMARK 3 REMARK 3 TLS GROUP : 1 REMARK 3 NUMBER OF COMPONENTS GROUP : 1 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : A 2 A 60 REMARK 3 ORIGIN FOR THE GROUP (A): 24.2348 -34.6778 -30.5145 REMARK 3 T TENSOR REMARK 3 T11: 0.2559 T22: 0.1880 REMARK 3 T33: 0.2632 T12: 0.0530 REMARK 3 T13: 0.0878 T23: 0.1702 REMARK 3 L TENSOR REMARK 3 L11: 3.1536 L22: 2.7058 REMARK 3 L33: 8.0787 L12: 0.0613 REMARK 3 L13: 2.6080 L23: 1.7306 REMARK 3 S TENSOR REMARK 3 S11: -0.0426 S12: -0.5322 S13: -0.6289 REMARK 3 S21: -0.4306 S22: 0.0824 S23: -0.0574 REMARK 3 S31: 0.5068 S32: 0.2046 S33: -0.0398 REMARK 3 REMARK 3 TLS GROUP : 2 REMARK 3 NUMBER OF COMPONENTS GROUP : 1 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : A 61 A 235 REMARK 3 ORIGIN FOR THE GROUP (A): 8.3543 -18.3850 -19.4449 REMARK 3 T TENSOR REMARK 3 T11: 0.1298 T22: 0.9297 REMARK 3 T33: 0.2925 T12: 0.1952 REMARK 3 T13: 0.0274 T23: -0.1210 REMARK 3 L TENSOR REMARK 3 L11: 3.2992 L22: 5.3919 REMARK 3 L33: 3.8120 L12: -0.6533 REMARK 3 L13: -0.9375 L23: 0.1810 REMARK 3 S TENSOR REMARK 3 S11: -0.0343 S12: -0.9993 S13: 0.1606 REMARK 3 S21: 0.3202 S22: -0.1577 S23: 0.8414 REMARK 3 S31: -0.5586 S32: -1.0809 S33: 0.1920 REMARK 3 REMARK 3 TLS GROUP : 3 REMARK 3 NUMBER OF COMPONENTS GROUP : 1 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : A 236 A 383 REMARK 3 ORIGIN FOR THE GROUP (A): 30.1153 -24.1241 -7.8777 REMARK 3 T TENSOR REMARK 3 T11: 0.3377 T22: 0.9175 REMARK 3 T33: 0.3098 T12: 0.0625 REMARK 3 T13: -0.0367 T23: 0.0173 REMARK 3 L TENSOR REMARK 3 L11: 2.8966 L22: 3.3464 REMARK 3 L33: 6.5898 L12: 0.3711 REMARK 3 L13: 2.0287 L23: 0.1360 REMARK 3 S TENSOR REMARK 3 S11: -0.0600 S12: -1.3633 S13: 0.2948 REMARK 3 S21: 1.0087 S22: -0.0897 S23: -0.2703 REMARK 3 S31: -0.2856 S32: -0.0771 S33: 0.1498 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: U VALUES : WITH TLS ADDED REMARK 4 REMARK 4 6KG1 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 18-JUL-19. REMARK 100 THE DEPOSITION ID IS D_1300012912. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 29-JUN-19 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 : PHOTON FACTORY REMARK 200 BEAMLINE : BL-17A REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.98 REMARK 200 MONOCHROMATOR : SI(111) DOUBLE CRYSTAL REMARK 200 MONOCHROMATOR REMARK 200 OPTICS : SI(111) DOUBLE CRYSTAL REMARK 200 MONOCHROMATOR REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS EIGER X 16M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : XSCALE REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 20267 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.700 REMARK 200 RESOLUTION RANGE LOW (A) : 49.180 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 100.0 REMARK 200 DATA REDUNDANCY : 7.086 REMARK 200 R MERGE (I) : 0.08300 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 14.1800 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.70 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.80 REMARK 200 COMPLETENESS FOR SHELL (%) : 100.0 REMARK 200 DATA REDUNDANCY IN SHELL : 7.33 REMARK 200 R MERGE FOR SHELL (I) : 0.78300 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 2.280 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: 5WT2 REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 69.22 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 4.00 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 17% (W/V) PEG 4000, 8.5% (V/V) 2 REMARK 280 -PROPANOL, 15% (V/V) GLYCEROL, 85MM HEPES-NAOH, PH 7.5, VAPOR REMARK 280 DIFFUSION, SITTING DROP, TEMPERATURE 293K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 41 21 2 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,-Y,Z+1/2 REMARK 290 3555 -Y+1/2,X+1/2,Z+1/4 REMARK 290 4555 Y+1/2,-X+1/2,Z+3/4 REMARK 290 5555 -X+1/2,Y+1/2,-Z+1/4 REMARK 290 6555 X+1/2,-Y+1/2,-Z+3/4 REMARK 290 7555 Y,X,-Z REMARK 290 8555 -Y,-X,-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 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 66.60000 REMARK 290 SMTRY1 3 0.000000 -1.000000 0.000000 51.45000 REMARK 290 SMTRY2 3 1.000000 0.000000 0.000000 51.45000 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 33.30000 REMARK 290 SMTRY1 4 0.000000 1.000000 0.000000 51.45000 REMARK 290 SMTRY2 4 -1.000000 0.000000 0.000000 51.45000 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 99.90000 REMARK 290 SMTRY1 5 -1.000000 0.000000 0.000000 51.45000 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 51.45000 REMARK 290 SMTRY3 5 0.000000 0.000000 -1.000000 33.30000 REMARK 290 SMTRY1 6 1.000000 0.000000 0.000000 51.45000 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 51.45000 REMARK 290 SMTRY3 6 0.000000 0.000000 -1.000000 99.90000 REMARK 290 SMTRY1 7 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY2 7 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 8 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY2 8 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 8 0.000000 0.000000 -1.000000 66.60000 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: 6320 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 26100 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -47.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: A REMARK 350 BIOMT1 1 1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT2 1 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT3 1 0.000000 0.000000 1.000000 0.00000 REMARK 350 BIOMT1 2 0.000000 -1.000000 0.000000 0.00000 REMARK 350 BIOMT2 2 -1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT3 2 0.000000 0.000000 -1.000000 -66.60000 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 CYS A 328 REMARK 465 ALA A 329 REMARK 465 SER A 330 REMARK 465 GLU A 331 REMARK 465 ASP A 332 REMARK 465 LEU A 333 REMARK 465 GLU A 334 REMARK 465 ALA A 335 REMARK 465 ASN A 336 REMARK 465 PRO A 337 REMARK 465 VAL A 338 REMARK 465 MET A 339 REMARK 465 VAL A 340 REMARK 465 ALA A 341 REMARK 465 ILE A 342 REMARK 465 GLY A 343 REMARK 465 ALA A 344 REMARK 465 SER A 345 REMARK 465 LYS A 346 REMARK 465 GLU A 347 REMARK 465 LEU A 348 REMARK 465 ALA A 349 REMARK 465 HIS A 350 REMARK 465 SER A 384 REMARK 465 SER A 385 REMARK 465 SER A 386 REMARK 465 TYR A 387 REMARK 465 VAL A 388 REMARK 465 ASP A 389 REMARK 465 LEU A 390 REMARK 465 VAL A 391 REMARK 465 PRO A 392 REMARK 465 ARG A 393 REMARK 465 GLY A 394 REMARK 465 SER A 395 REMARK 465 HIS A 396 REMARK 465 HIS A 397 REMARK 465 HIS A 398 REMARK 465 HIS A 399 REMARK 465 HIS A 400 REMARK 465 HIS A 401 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 GLU A 43 CD GLU A 43 OE1 0.084 REMARK 500 GLU A 43 CD GLU A 43 OE2 0.100 REMARK 500 GLU A 103 CD GLU A 103 OE1 0.108 REMARK 500 GLU A 139 CD GLU A 139 OE2 0.069 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 ARG A 4 CB - CA - C ANGL. DEV. = 17.9 DEGREES REMARK 500 ARG A 4 NE - CZ - NH1 ANGL. DEV. = -5.7 DEGREES REMARK 500 ARG A 14 CG - CD - NE ANGL. DEV. = 16.1 DEGREES REMARK 500 ARG A 28 CB - CA - C ANGL. DEV. = 15.8 DEGREES REMARK 500 ARG A 28 NE - CZ - NH1 ANGL. DEV. = -3.8 DEGREES REMARK 500 ASN A 60 CB - CA - C ANGL. DEV. = 12.1 DEGREES REMARK 500 ARG A 108 NE - CZ - NH2 ANGL. DEV. = -3.6 DEGREES REMARK 500 ARG A 138 CB - CG - CD ANGL. DEV. = 19.0 DEGREES REMARK 500 LYS A 173 CB - CA - C ANGL. DEV. = 18.1 DEGREES REMARK 500 LYS A 173 CB - CG - CD ANGL. DEV. = 15.9 DEGREES REMARK 500 MET A 250 CG - SD - CE ANGL. DEV. = -12.2 DEGREES REMARK 500 LYS A 270 CB - CA - C ANGL. DEV. = 14.5 DEGREES REMARK 500 PRO A 283 N - CA - CB ANGL. DEV. = -7.4 DEGREES REMARK 500 PRO A 283 N - CD - CG ANGL. DEV. = -9.9 DEGREES REMARK 500 GLU A 371 CB - CA - C ANGL. DEV. = 12.7 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 ASP A 8 38.60 -140.81 REMARK 500 THR A 12 -177.76 -175.38 REMARK 500 ARG A 28 -94.53 -106.83 REMARK 500 HIS A 30 69.97 -102.70 REMARK 500 ILE A 64 5.75 -69.15 REMARK 500 CYS A 72 171.86 169.71 REMARK 500 ALA A 134 -62.36 102.04 REMARK 500 ILE A 141 104.17 -53.28 REMARK 500 PRO A 162 41.52 -79.14 REMARK 500 ILE A 163 142.04 -36.30 REMARK 500 GLU A 164 -71.33 101.71 REMARK 500 ASN A 196 49.85 33.63 REMARK 500 SER A 220 119.43 -21.37 REMARK 500 LEU A 224 99.49 -161.91 REMARK 500 ILE A 282 -91.99 -90.05 REMARK 500 PRO A 283 -89.83 -134.64 REMARK 500 ASP A 284 56.54 -98.55 REMARK 500 HIS A 293 54.24 -99.71 REMARK 500 ARG A 381 -81.00 -40.62 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 IPA A 501 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue CL A 502 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue PDA A 503 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 5WT2 RELATED DB: PDB DBREF 6KG1 A 1 387 UNP O25008 ISCS_HELPY 1 387 SEQADV 6KG1 VAL A 2 UNP O25008 LEU 2 ENGINEERED MUTATION SEQADV 6KG1 ARG A 138 UNP O25008 LYS 138 ENGINEERED MUTATION SEQADV 6KG1 VAL A 388 UNP O25008 EXPRESSION TAG SEQADV 6KG1 ASP A 389 UNP O25008 EXPRESSION TAG SEQADV 6KG1 LEU A 390 UNP O25008 EXPRESSION TAG SEQADV 6KG1 VAL A 391 UNP O25008 EXPRESSION TAG SEQADV 6KG1 PRO A 392 UNP O25008 EXPRESSION TAG SEQADV 6KG1 ARG A 393 UNP O25008 EXPRESSION TAG SEQADV 6KG1 GLY A 394 UNP O25008 EXPRESSION TAG SEQADV 6KG1 SER A 395 UNP O25008 EXPRESSION TAG SEQADV 6KG1 HIS A 396 UNP O25008 EXPRESSION TAG SEQADV 6KG1 HIS A 397 UNP O25008 EXPRESSION TAG SEQADV 6KG1 HIS A 398 UNP O25008 EXPRESSION TAG SEQADV 6KG1 HIS A 399 UNP O25008 EXPRESSION TAG SEQADV 6KG1 HIS A 400 UNP O25008 EXPRESSION TAG SEQADV 6KG1 HIS A 401 UNP O25008 EXPRESSION TAG SEQRES 1 A 401 MET VAL GLN ARG ILE TYR LEU ASP ASN ASN ALA THR THR SEQRES 2 A 401 ARG ILE ASP PRO LYS VAL LYS GLU ILE MET ASP PRO PHE SEQRES 3 A 401 LEU ARG ASP HIS TYR GLY ASN PRO SER SER LEU HIS GLN SEQRES 4 A 401 PHE GLY THR GLU THR HIS PRO ALA ILE ALA GLU ALA LEU SEQRES 5 A 401 ASP LYS LEU TYR LYS GLY ILE ASN ALA ARG ASP ILE ASP SEQRES 6 A 401 ASP VAL ILE ILE THR SER CYS ALA THR GLU SER ASN ASN SEQRES 7 A 401 TRP VAL LEU LYS GLY VAL TYR PHE ASP GLU CYS LEU LYS SEQRES 8 A 401 LYS GLY LYS ASN HIS ILE VAL THR THR VAL ALA GLU HIS SEQRES 9 A 401 PRO ALA VAL ARG SER THR CYS ASN PHE LEU GLU SER LEU SEQRES 10 A 401 GLY VAL GLU VAL THR TYR LEU PRO ILE ASN GLU HIS GLY SEQRES 11 A 401 SER ILE THR ALA GLU GLN VAL ARG GLU ALA ILE THR GLU SEQRES 12 A 401 LYS THR ALA LEU VAL SER VAL MET TRP ALA ASN ASN GLU SEQRES 13 A 401 THR GLY LEU ILE PHE PRO ILE GLU GLU ILE GLY ALA ILE SEQRES 14 A 401 CYS LYS GLU LYS GLY VAL LEU PHE HIS THR ASP ALA VAL SEQRES 15 A 401 GLN ALA ILE GLY LYS ILE PRO VAL ASP VAL LEU LYS ALA SEQRES 16 A 401 ASN ALA ASP PHE LEU SER PHE SER ALA HIS LYS PHE HIS SEQRES 17 A 401 GLY PRO LYS GLY ILE GLY GLY LEU TYR ILE ARG SER GLY SEQRES 18 A 401 VAL GLY LEU THR PRO LEU PHE HIS GLY GLY GLU HIS MET SEQRES 19 A 401 ASN GLY ARG ARG SER GLY THR LEU ASN VAL PRO TYR ILE SEQRES 20 A 401 VAL GLY MET GLY GLU ALA MET LYS LEU ALA VAL GLU HIS SEQRES 21 A 401 LEU ASP TYR GLU LYS GLU VAL VAL GLY LYS LEU ARG ASP SEQRES 22 A 401 LYS LEU GLU GLU ALA LEU LEU LYS ILE PRO ASP VAL MET SEQRES 23 A 401 VAL VAL GLY ASP ARG ILE HIS ARG VAL PRO ASN THR THR SEQRES 24 A 401 LEU VAL SER VAL ARG GLY ILE GLU GLY GLU ALA MET LEU SEQRES 25 A 401 TRP ASP LEU ASN ARG SER ASN ILE ALA ALA SER THR GLY SEQRES 26 A 401 SER ALA CYS ALA SER GLU ASP LEU GLU ALA ASN PRO VAL SEQRES 27 A 401 MET VAL ALA ILE GLY ALA SER LYS GLU LEU ALA HIS THR SEQRES 28 A 401 ALA ILE ARG LEU SER LEU SER ARG PHE ASN THR GLU ALA SEQRES 29 A 401 GLU ILE ASP LYS THR ILE GLU VAL PHE SER GLN ALA ALA SEQRES 30 A 401 VAL ARG LEU ARG ASN ILE SER SER SER TYR VAL ASP LEU SEQRES 31 A 401 VAL PRO ARG GLY SER HIS HIS HIS HIS HIS HIS HET IPA A 501 4 HET CL A 502 1 HET PDA A 503 21 HETNAM IPA ISOPROPYL ALCOHOL HETNAM CL CHLORIDE ION HETNAM PDA 2-[(3-HYDROXY-2-METHYL-5-PHOSPHONOOXYMETHYL-PYRIDIN-4- HETNAM 2 PDA YLMETHYL)-AMINO]-PROPIONIC ACID HETSYN IPA 2-PROPANOL HETSYN PDA PYRIDOXYL-ALANINE-5-PHOSPHATE FORMUL 2 IPA C3 H8 O FORMUL 3 CL CL 1- FORMUL 4 PDA C11 H17 N2 O7 P FORMUL 5 HOH *8(H2 O) HELIX 1 AA1 ASP A 16 ARG A 28 1 13 HELIX 2 AA2 HIS A 38 GLU A 43 1 6 HELIX 3 AA3 THR A 44 ILE A 59 1 16 HELIX 4 AA4 CYS A 72 GLU A 88 1 17 HELIX 5 AA5 HIS A 104 GLY A 118 1 15 HELIX 6 AA6 ALA A 134 GLU A 139 1 6 HELIX 7 AA7 GLU A 164 GLY A 174 1 11 HELIX 8 AA8 HIS A 205 HIS A 208 5 4 HELIX 9 AA9 HIS A 233 ARG A 237 5 5 HELIX 10 AB1 ASN A 243 HIS A 260 1 18 HELIX 11 AB2 HIS A 260 VAL A 267 1 8 HELIX 12 AB3 VAL A 267 LYS A 281 1 15 HELIX 13 AB4 GLU A 307 SER A 318 1 12 HELIX 14 AB5 THR A 362 ARG A 381 1 20 SHEET 1 AA1 2 ILE A 5 TYR A 6 0 SHEET 2 AA1 2 ILE A 320 ALA A 321 1 O ALA A 321 N ILE A 5 SHEET 1 AA2 7 ASP A 66 THR A 70 0 SHEET 2 AA2 7 GLY A 214 ILE A 218 -1 O GLY A 214 N THR A 70 SHEET 3 AA2 7 PHE A 199 SER A 203 -1 N LEU A 200 O TYR A 217 SHEET 4 AA2 7 LEU A 176 ASP A 180 1 N THR A 179 O PHE A 199 SHEET 5 AA2 7 THR A 145 SER A 149 1 N VAL A 148 O HIS A 178 SHEET 6 AA2 7 HIS A 96 THR A 100 1 N HIS A 96 O ALA A 146 SHEET 7 AA2 7 GLU A 120 LEU A 124 1 O LEU A 124 N THR A 99 SHEET 1 AA3 3 THR A 298 VAL A 301 0 SHEET 2 AA3 3 ALA A 352 SER A 356 -1 O ILE A 353 N VAL A 301 SHEET 3 AA3 3 SER A 323 GLY A 325 -1 N SER A 323 O ARG A 354 SITE 1 AC1 4 TYR A 56 ASP A 66 VAL A 67 ILE A 68 SITE 1 AC2 1 PRO A 226 SITE 1 AC3 15 ASN A 10 CYS A 72 ALA A 73 THR A 74 SITE 2 AC3 15 HIS A 104 ASN A 155 ASP A 180 VAL A 182 SITE 3 AC3 15 GLN A 183 SER A 203 HIS A 205 LYS A 206 SITE 4 AC3 15 GLY A 240 THR A 241 ARG A 354 CRYST1 102.900 102.900 133.200 90.00 90.00 90.00 P 41 21 2 8 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 0.009718 0.000000 0.000000 0.00000 SCALE2 0.000000 0.009718 0.000000 0.00000 SCALE3 0.000000 0.000000 0.007508 0.00000