HEADER TRANSFERASE 06-NOV-12 4HVK TITLE CRYSTAL STRUCTURE AND FUNCTIONAL STUDIES OF AN UNUSUAL L-CYSTEINE TITLE 2 DESULFURASE FROM ARCHAEOGLOBUS FULGIDUS. COMPND MOL_ID: 1; COMPND 2 MOLECULE: PROBABLE CYSTEINE DESULFURASE 2; COMPND 3 CHAIN: A; COMPND 4 EC: 2.8.1.7; COMPND 5 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: ARCHAEOGLOBUS FULGIDUS; SOURCE 3 ORGANISM_TAXID: 224325; SOURCE 4 STRAIN: ATCC 49558 / VC-16 / DSM 4304 / JCM 9628 / NBRC 100126; SOURCE 5 GENE: AF0564, AF_0564, ISCS2; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 8 EXPRESSION_SYSTEM_STRAIN: C41 KEYWDS TRANSFERASE AND ISCS, TRANSFERASE EXPDTA X-RAY DIFFRACTION AUTHOR Y.YAMANAKA,L.ZEPPIERI,Y.NICOLET,E.N.MARINONI,J.S.DE OLIVEIRA, AUTHOR 2 O.MASAFUMI,D.R.DEAN,J.C.FONTECILLA-CAMPS REVDAT 3 28-FEB-24 4HVK 1 REMARK LINK REVDAT 2 24-APR-13 4HVK 1 JRNL REVDAT 1 05-DEC-12 4HVK 0 JRNL AUTH Y.YAMANAKA,L.ZEPPIERI,Y.NICOLET,E.N.MARINONI, JRNL AUTH 2 J.S.DE OLIVEIRA,M.ODAKA,D.R.DEAN,J.C.FONTECILLA-CAMPS JRNL TITL CRYSTAL STRUCTURE AND FUNCTIONAL STUDIES OF AN UNUSUAL JRNL TITL 2 L-CYSTEINE DESULFURASE FROM ARCHAEOGLOBUS FULGIDUS. JRNL REF DALTON TRANS V. 42 3092 2013 JRNL REFN ISSN 1477-9226 JRNL PMID 23160436 JRNL DOI 10.1039/C2DT32101G REMARK 2 REMARK 2 RESOLUTION. 1.43 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.6.0117 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) : 1.43 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 57.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 98.3 REMARK 3 NUMBER OF REFLECTIONS : 65502 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) : 0.110 REMARK 3 R VALUE (WORKING SET) : 0.108 REMARK 3 FREE R VALUE : 0.151 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.000 REMARK 3 FREE R VALUE TEST SET COUNT : 3477 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) : 1.43 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.47 REMARK 3 REFLECTION IN BIN (WORKING SET) : 3923 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 83.43 REMARK 3 BIN R VALUE (WORKING SET) : 0.1600 REMARK 3 BIN FREE R VALUE SET COUNT : 210 REMARK 3 BIN FREE R VALUE : 0.2200 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 2794 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 101 REMARK 3 SOLVENT ATOMS : 379 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 16.13 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -0.92000 REMARK 3 B22 (A**2) : 1.33000 REMARK 3 B33 (A**2) : -0.41000 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): 0.052 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.051 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.031 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 1.752 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.982 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.972 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 3253 ; 0.023 ; 0.019 REMARK 3 BOND LENGTHS OTHERS (A): 2224 ; 0.002 ; 0.020 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 4412 ; 2.225 ; 1.990 REMARK 3 BOND ANGLES OTHERS (DEGREES): 5496 ; 1.172 ; 3.000 REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 434 ; 6.393 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 138 ;37.831 ;24.855 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 568 ;11.624 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 23 ;15.806 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 496 ; 0.142 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 3683 ; 0.012 ; 0.020 REMARK 3 GENERAL PLANES OTHERS (A): 613 ; 0.005 ; 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): 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): 5470 ; 6.996 ; 3.000 REMARK 3 SPHERICITY; FREE ATOMS (A**2): 87 ;32.553 ; 5.000 REMARK 3 SPHERICITY; BONDED ATOMS (A**2): 5700 ;10.855 ; 5.000 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 : BABINET MODEL WITH MASK 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 4HVK COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 07-NOV-12. REMARK 100 THE DEPOSITION ID IS D_1000075974. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 05-NOV-09 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 6.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : ESRF REMARK 200 BEAMLINE : ID14-4 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.939 REMARK 200 MONOCHROMATOR : DIAMOND REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 4 REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : XSCALE REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 70218 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.430 REMARK 200 RESOLUTION RANGE LOW (A) : 57.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 0.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 98.3 REMARK 200 DATA REDUNDANCY : NULL REMARK 200 R MERGE (I) : NULL 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) : 1.43 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.47 REMARK 200 COMPLETENESS FOR SHELL (%) : 84.4 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: PHASER REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 45.56 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.26 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 200 MM CALCIUM ACETATE; 100 MM SODIUM REMARK 280 CACODYLATE; 40% PEG 300 , PH 6.5, VAPOR DIFFUSION, HANGING DROP, REMARK 280 TEMPERATURE 293K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: C 2 2 21 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 -X,Y,-Z+1/2 REMARK 290 4555 X,-Y,-Z REMARK 290 5555 X+1/2,Y+1/2,Z REMARK 290 6555 -X+1/2,-Y+1/2,Z+1/2 REMARK 290 7555 -X+1/2,Y+1/2,-Z+1/2 REMARK 290 8555 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 0.00000 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 54.43000 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 54.43000 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 4 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 5 1.000000 0.000000 0.000000 35.03000 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 49.63500 REMARK 290 SMTRY3 5 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 6 -1.000000 0.000000 0.000000 35.03000 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 49.63500 REMARK 290 SMTRY3 6 0.000000 0.000000 1.000000 54.43000 REMARK 290 SMTRY1 7 -1.000000 0.000000 0.000000 35.03000 REMARK 290 SMTRY2 7 0.000000 1.000000 0.000000 49.63500 REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 54.43000 REMARK 290 SMTRY1 8 1.000000 0.000000 0.000000 35.03000 REMARK 290 SMTRY2 8 0.000000 -1.000000 0.000000 49.63500 REMARK 290 SMTRY3 8 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: 11750 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 26890 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -57.0 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 -1.000000 0.000000 0.000000 70.06000 REMARK 350 BIOMT2 2 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT3 2 0.000000 0.000000 -1.000000 54.43000 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 SER A 319 REMARK 465 ALA A 320 REMARK 465 CYS A 321 REMARK 465 SER A 322 REMARK 465 SER A 323 REMARK 465 LYS A 324 REMARK 465 THR A 325 REMARK 465 LEU A 326 REMARK 465 LEU A 379 REMARK 465 TYR A 380 REMARK 465 ARG A 381 REMARK 465 ARG A 382 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 GLU A 14 CG CD OE1 OE2 REMARK 470 LYS A 40 CE NZ REMARK 470 ARG A 42 NE CZ NH1 NH2 REMARK 470 ARG A 86 NH1 NH2 REMARK 470 LYS A 122 NZ REMARK 470 ASP A 137 OD1 OD2 REMARK 470 LYS A 216 CE NZ REMARK 470 GLU A 302 CG CD OE1 OE2 REMARK 470 GLN A 327 CG CD OE1 NE2 REMARK 470 HIS A 339 CG ND1 CD2 CE1 NE2 REMARK 470 GLU A 340 CG CD OE1 OE2 REMARK 470 HIS A 343 CG ND1 CD2 CE1 NE2 REMARK 470 GLU A 371 CD OE1 OE2 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 OG1 THR A 25 O HOH A 824 1.40 REMARK 500 NH1 ARG A 231 O HOH A 807 1.67 REMARK 500 CG1 VAL A 220 O HOH A 614 1.85 REMARK 500 NZ LYS A 51 O HOH A 774 1.91 REMARK 500 O2 PG4 A 408 O HOH A 828 1.94 REMARK 500 CE LYS A 122 O HOH A 789 1.94 REMARK 500 OD1 ASP A 270 O HOH A 819 1.94 REMARK 500 O2P PMP A 404 O HOH A 825 2.10 REMARK 500 C GLY A 318 O HOH A 816 2.11 REMARK 500 O HOH A 735 O HOH A 787 2.14 REMARK 500 O HOH A 767 O HOH A 853 2.14 REMARK 500 O HOH A 758 O HOH A 780 2.15 REMARK 500 O HOH A 796 O HOH A 876 2.16 REMARK 500 OE1 GLU A 300 O HOH A 820 2.17 REMARK 500 O HOH A 744 O HOH A 754 2.19 REMARK 500 OE2 GLU A 159 O HOH A 679 2.19 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 A 869 O HOH A 869 4555 1.73 REMARK 500 CE MET A 376 O HOH A 572 1455 1.93 REMARK 500 CE MET A 376 O HOH A 749 3555 2.02 REMARK 500 O HOH A 630 O HOH A 630 3655 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 GLU A 50 CD GLU A 50 OE1 0.081 REMARK 500 GLU A 125 CD GLU A 125 OE2 0.079 REMARK 500 GLU A 259 CD GLU A 259 OE2 0.071 REMARK 500 SER A 316 CA SER A 316 CB 0.107 REMARK 500 SER A 316 CB SER A 316 OG -0.106 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 GLU A 47 OE1 - CD - OE2 ANGL. DEV. = -7.4 DEGREES REMARK 500 ARG A 255 NE - CZ - NH1 ANGL. DEV. = 3.4 DEGREES REMARK 500 GLU A 259 OE1 - CD - OE2 ANGL. DEV. = 8.6 DEGREES REMARK 500 ARG A 295 NE - CZ - NH1 ANGL. DEV. = -3.1 DEGREES REMARK 500 ARG A 352 NE - CZ - NH1 ANGL. DEV. = 4.0 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 ALA A 9 145.86 -177.38 REMARK 500 SER A 27 72.58 -105.53 REMARK 500 VAL A 34 61.40 -105.06 REMARK 500 VAL A 34 45.16 -103.98 REMARK 500 ALA A 165 73.89 -26.74 REMARK 500 GLU A 214 -10.48 84.24 REMARK 500 TYR A 298 -7.84 83.07 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: NON-CIS, NON-TRANS REMARK 500 REMARK 500 THE FOLLOWING PEPTIDE BONDS DEVIATE SIGNIFICANTLY FROM BOTH REMARK 500 CIS AND TRANS CONFORMATION. CIS BONDS, IF ANY, ARE LISTED REMARK 500 ON CISPEP RECORDS. TRANS IS DEFINED AS 180 +/- 30 AND REMARK 500 CIS IS DEFINED AS 0 +/- 30 DEGREES. REMARK 500 MODEL OMEGA REMARK 500 ALA A 165 GLY A 166 134.08 REMARK 500 REMARK 500 REMARK: NULL REMARK 610 REMARK 610 MISSING HETEROATOM REMARK 610 THE FOLLOWING RESIDUES HAVE MISSING ATOMS (M=MODEL NUMBER; REMARK 610 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; REMARK 610 I=INSERTION CODE): REMARK 610 M RES C SSEQI REMARK 610 PG4 A 406 REMARK 610 PG4 A 407 REMARK 610 PG4 A 408 REMARK 610 PG4 A 409 REMARK 610 PG4 A 410 REMARK 610 PG4 A 411 REMARK 610 PG4 A 412 REMARK 610 PG4 A 414 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 CA A 401 CA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 PG4 A 405 O2 REMARK 620 2 PG4 A 405 O3 67.9 REMARK 620 3 PG4 A 405 O4 135.7 69.5 REMARK 620 4 PG4 A 405 O5 141.4 115.2 70.1 REMARK 620 5 PG4 A 405 O1 60.6 128.3 156.0 108.1 REMARK 620 6 HOH A 814 O 84.4 89.4 83.5 132.6 81.0 REMARK 620 N 1 2 3 4 5 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CA A 401 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CL A 402 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CA A 403 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE PMP A 404 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE PG4 A 405 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE PG4 A 406 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC7 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE PG4 A 407 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC8 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE PG4 A 408 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC9 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE PG4 A 409 REMARK 800 REMARK 800 SITE_IDENTIFIER: BC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE PG4 A 410 REMARK 800 REMARK 800 SITE_IDENTIFIER: BC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE PG4 A 411 REMARK 800 REMARK 800 SITE_IDENTIFIER: BC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE PG4 A 412 REMARK 800 REMARK 800 SITE_IDENTIFIER: BC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE PG4 A 413 REMARK 800 REMARK 800 SITE_IDENTIFIER: BC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE PG4 A 414 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 4EB5 RELATED DB: PDB REMARK 900 COMPLEX BETWEEN THE CYSTEINE DESULFURASE AND THE SCAFFOLD PROTEIN REMARK 900 ISCU REMARK 900 RELATED ID: 4EB7 RELATED DB: PDB REMARK 900 COMPLEX BETWEEN THE CYSTEINE DESULFURASE AND THE SCAFFOLD PROTEIN REMARK 900 ISCU REMARK 999 REMARK 999 SEQUENCE REMARK 999 AUTHORS STATE THAT THE CORRECTNESS OF THE SIDE CHAIN COULD BE REMARK 999 DETERMINED BY INSPECTING THE ELECTRON DENSITY DBREF 4HVK A 1 382 UNP O29689 ISCS2_ARCFU 1 382 SEQADV 4HVK ILE A 16 UNP O29689 VAL 16 SEE REMARK 999 SEQRES 1 A 382 MET ALA TYR PHE ASP TYR THR SER ALA LYS PRO VAL ASP SEQRES 2 A 382 GLU ARG ILE LEU GLU ALA MET LEU PRO TYR MET THR GLU SEQRES 3 A 382 SER PHE GLY ASN PRO SER SER VAL HIS SER TYR GLY PHE SEQRES 4 A 382 LYS ALA ARG GLU ALA VAL GLN GLU ALA ARG GLU LYS VAL SEQRES 5 A 382 ALA LYS LEU VAL ASN GLY GLY GLY GLY THR VAL VAL PHE SEQRES 6 A 382 THR SER GLY ALA THR GLU ALA ASN ASN LEU ALA ILE ILE SEQRES 7 A 382 GLY TYR ALA MET ARG ASN ALA ARG LYS GLY LYS HIS ILE SEQRES 8 A 382 LEU VAL SER ALA VAL GLU HIS MET SER VAL ILE ASN PRO SEQRES 9 A 382 ALA LYS PHE LEU GLN LYS GLN GLY PHE GLU VAL GLU TYR SEQRES 10 A 382 ILE PRO VAL GLY LYS TYR GLY GLU VAL ASP VAL SER PHE SEQRES 11 A 382 ILE ASP GLN LYS LEU ARG ASP ASP THR ILE LEU VAL SER SEQRES 12 A 382 VAL GLN HIS ALA ASN ASN GLU ILE GLY THR ILE GLN PRO SEQRES 13 A 382 VAL GLU GLU ILE SER GLU VAL LEU ALA GLY LYS ALA ALA SEQRES 14 A 382 LEU HIS ILE ASP ALA THR ALA SER VAL GLY GLN ILE GLU SEQRES 15 A 382 VAL ASP VAL GLU LYS ILE GLY ALA ASP MET LEU THR ILE SEQRES 16 A 382 SER SER ASN ASP ILE TYR GLY PRO LYS GLY VAL GLY ALA SEQRES 17 A 382 LEU TRP ILE ARG LYS GLU ALA LYS LEU GLN PRO VAL ILE SEQRES 18 A 382 LEU GLY GLY GLY GLN GLU ASN GLY LEU ARG SER GLY SER SEQRES 19 A 382 GLU ASN VAL PRO SER ILE VAL GLY PHE GLY LYS ALA ALA SEQRES 20 A 382 GLU ILE THR ALA MET GLU TRP ARG GLU GLU ALA GLU ARG SEQRES 21 A 382 LEU ARG ARG LEU ARG ASP ARG ILE ILE ASP ASN VAL LEU SEQRES 22 A 382 LYS ILE GLU GLU SER TYR LEU ASN GLY HIS PRO GLU LYS SEQRES 23 A 382 ARG LEU PRO ASN ASN VAL ASN VAL ARG PHE SER TYR ILE SEQRES 24 A 382 GLU GLY GLU SER ILE VAL LEU SER LEU ASP MET ALA GLY SEQRES 25 A 382 ILE GLN ALA SER THR GLY SER ALA CYS SER SER LYS THR SEQRES 26 A 382 LEU GLN PRO SER HIS VAL LEU MET ALA CYS GLY LEU LYS SEQRES 27 A 382 HIS GLU GLU ALA HIS GLY THR LEU LEU LEU THR LEU GLY SEQRES 28 A 382 ARG TYR ASN THR ASP GLU ASP VAL ASP ARG LEU LEU GLU SEQRES 29 A 382 VAL LEU PRO GLY VAL ILE GLU ARG LEU ARG SER MET SER SEQRES 30 A 382 PRO LEU TYR ARG ARG HET CA A 401 1 HET CL A 402 1 HET CA A 403 1 HET PMP A 404 16 HET PG4 A 405 13 HET PG4 A 406 7 HET PG4 A 407 10 HET PG4 A 408 10 HET PG4 A 409 7 HET PG4 A 410 6 HET PG4 A 411 4 HET PG4 A 412 4 HET PG4 A 413 13 HET PG4 A 414 8 HETNAM CA CALCIUM ION HETNAM CL CHLORIDE ION HETNAM PMP 4'-DEOXY-4'-AMINOPYRIDOXAL-5'-PHOSPHATE HETNAM PG4 TETRAETHYLENE GLYCOL HETSYN PMP PYRIDOXAMINE-5'-PHOSPHATE FORMUL 2 CA 2(CA 2+) FORMUL 3 CL CL 1- FORMUL 5 PMP C8 H13 N2 O5 P FORMUL 6 PG4 10(C8 H18 O5) FORMUL 16 HOH *379(H2 O) HELIX 1 1 ASP A 13 GLU A 26 1 14 HELIX 2 2 HIS A 35 VAL A 56 1 22 HELIX 3 3 GLY A 68 ALA A 85 1 18 HELIX 4 4 ARG A 86 GLY A 88 5 3 HELIX 5 5 HIS A 98 GLN A 111 1 14 HELIX 6 6 ASP A 127 LEU A 135 1 9 HELIX 7 7 PRO A 156 ALA A 165 1 10 HELIX 8 8 ASP A 184 GLY A 189 1 6 HELIX 9 9 ASN A 198 TYR A 201 5 4 HELIX 10 10 GLN A 226 LEU A 230 5 5 HELIX 11 11 ASN A 236 LEU A 273 1 38 HELIX 12 12 GLU A 300 ALA A 311 1 12 HELIX 13 13 SER A 329 CYS A 335 1 7 HELIX 14 14 LYS A 338 GLY A 344 1 7 HELIX 15 15 THR A 355 MET A 376 1 22 SHEET 1 A 7 GLY A 61 THR A 66 0 SHEET 2 A 7 GLY A 207 ARG A 212 -1 O ILE A 211 N THR A 62 SHEET 3 A 7 MET A 192 SER A 196 -1 N ILE A 195 O ALA A 208 SHEET 4 A 7 ALA A 169 ASP A 173 1 N ILE A 172 O MET A 192 SHEET 5 A 7 THR A 139 SER A 143 1 N VAL A 142 O HIS A 171 SHEET 6 A 7 HIS A 90 SER A 94 1 N LEU A 92 O SER A 143 SHEET 7 A 7 GLU A 114 ILE A 118 1 O GLU A 114 N ILE A 91 SHEET 1 B 3 SER A 278 LEU A 280 0 SHEET 2 B 3 ASN A 291 PHE A 296 -1 O ARG A 295 N TYR A 279 SHEET 3 B 3 THR A 345 THR A 349 -1 O LEU A 348 N VAL A 292 LINK OD2 ASP A 173 CA B CA A 403 1555 1555 2.77 LINK CA CA A 401 O2 PG4 A 405 1555 1555 2.47 LINK CA CA A 401 O3 PG4 A 405 1555 1555 2.52 LINK CA CA A 401 O4 PG4 A 405 1555 1555 2.81 LINK CA CA A 401 O5 PG4 A 405 1555 1555 2.84 LINK CA CA A 401 O1 PG4 A 405 1555 1555 2.91 LINK CA CA A 401 O HOH A 814 1555 1555 2.31 SITE 1 AC1 2 PG4 A 405 HOH A 814 SITE 1 AC2 6 GLY A 121 LYS A 122 TYR A 123 GLY A 124 SITE 2 AC2 6 GLU A 125 HOH A 829 SITE 1 AC3 4 ASN A 73 HIS A 98 ASP A 173 THR A 175 SITE 1 AC4 21 THR A 7 ALA A 69 THR A 70 ASN A 73 SITE 2 AC4 21 HIS A 98 SER A 100 ASN A 149 ASP A 173 SITE 3 AC4 21 THR A 175 SER A 234 HOH A 509 HOH A 556 SITE 4 AC4 21 HOH A 585 HOH A 593 HOH A 665 HOH A 709 SITE 5 AC4 21 HOH A 790 HOH A 825 HOH A 826 HOH A 827 SITE 6 AC4 21 HOH A 867 SITE 1 AC5 6 TYR A 123 GLY A 166 LYS A 213 PRO A 284 SITE 2 AC5 6 CA A 401 HOH A 764 SITE 1 AC6 8 LEU A 55 VAL A 178 GLY A 179 ILE A 181 SITE 2 AC6 8 GLU A 182 VAL A 183 TRP A 254 HOH A 870 SITE 1 AC7 2 GLU A 26 LYS A 40 SITE 1 AC8 5 ASN A 103 LYS A 110 LEU A 222 PG4 A 410 SITE 2 AC8 5 HOH A 828 SITE 1 AC9 3 ILE A 102 LYS A 106 TYR A 117 SITE 1 BC1 4 LYS A 110 PG4 A 408 HOH A 775 HOH A 828 SITE 1 BC2 2 ARG A 295 GLU A 341 SITE 1 BC3 1 TYR A 298 SITE 1 BC4 4 ARG A 15 ALA A 19 LYS A 245 GLU A 248 SITE 1 BC5 4 THR A 25 TYR A 353 HOH A 730 HOH A 864 CRYST1 70.060 99.270 108.860 90.00 90.00 90.00 C 2 2 21 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 0.014273 0.000000 0.000000 0.00000 SCALE2 0.000000 0.010074 0.000000 0.00000 SCALE3 0.000000 0.000000 0.009186 0.00000