HEADER LIGASE 02-MAR-09 3A04 TITLE CRYSTAL STRUCTURE OF TRYPTOPHANYL-TRNA SYNTHETASE FROM TITLE 2 HYPERTHERMOPHILIC ARCHAEON, AEROPYRUM PERNIX K1 COMPND MOL_ID: 1; COMPND 2 MOLECULE: TRYPTOPHANYL-TRNA SYNTHETASE; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: TRYPTOPHAN-TRNA LIGASE, TRPRS; COMPND 5 EC: 6.1.1.2; COMPND 6 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: AEROPYRUM PERNIX; SOURCE 3 ORGANISM_TAXID: 56636; SOURCE 4 STRAIN: K1; SOURCE 5 GENE: TRPS, APE_2461.1; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 8 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 9 EXPRESSION_SYSTEM_PLASMID: PET30A KEYWDS TRYPTOPHANYL-TRNA SYNTHETASE, LIGASE, AMINOACYL-TRNA SYNTHETASE, ATP- KEYWDS 2 BINDING, CYTOPLASM, NUCLEOTIDE-BINDING, PROTEIN BIOSYNTHESIS EXPDTA X-RAY DIFFRACTION AUTHOR W.TSUCHIYA,Z.FUJIMOTO,T.HASEGAWA REVDAT 3 03-APR-24 3A04 1 REMARK REVDAT 2 13-MAR-24 3A04 1 REMARK LINK REVDAT 1 09-MAR-10 3A04 0 JRNL AUTH W.TSUCHIYA,Z.FUJIMOTO,T.HASEGAWA JRNL TITL CRYSTAL STRUCTURE OF TRYPTOPHANYL-TRNA SYNTHETASE FROM JRNL TITL 2 HYPERTHERMOPHILIC ARCHAEON, AEROPYRUM PERNIX K1 JRNL REF TO BE PUBLISHED JRNL REFN REMARK 1 REMARK 1 REFERENCE 1 REMARK 1 AUTH W.TSUCHIYA,T.HASEGAWA REMARK 1 TITL MOLECULAR RECOGNITION OF TRYPTOPHAN TRNA BY REMARK 1 TITL 2 TRYPTOPHANYL-TRNA SYNTHETASE FROM AEROPYRUM PERNIX K1 REMARK 1 REF J.BIOCHEM. 2009 REMARK 1 REFN ISSN 0021-924X REMARK 1 PMID 19179361 REMARK 1 DOI 10.1093/JB/MVP020 REMARK 2 REMARK 2 RESOLUTION. 1.97 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.5.0072 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) : 1.97 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 32.48 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 99.1 REMARK 3 NUMBER OF REFLECTIONS : 33531 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) : 0.180 REMARK 3 R VALUE (WORKING SET) : 0.178 REMARK 3 FREE R VALUE : 0.235 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.000 REMARK 3 FREE R VALUE TEST SET COUNT : 1762 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) : 1.97 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.02 REMARK 3 REFLECTION IN BIN (WORKING SET) : 2273 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 91.99 REMARK 3 BIN R VALUE (WORKING SET) : 0.2300 REMARK 3 BIN FREE R VALUE SET COUNT : 116 REMARK 3 BIN FREE R VALUE : 0.2810 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 2926 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 10 REMARK 3 SOLVENT ATOMS : 329 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 42.80 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -3.43000 REMARK 3 B22 (A**2) : 2.16000 REMARK 3 B33 (A**2) : 1.26000 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): 0.143 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.148 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.095 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 3.306 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.944 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.936 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 2985 ; 0.027 ; 0.022 REMARK 3 BOND LENGTHS OTHERS (A): NULL ; NULL ; NULL REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 4036 ; 2.016 ; 1.977 REMARK 3 BOND ANGLES OTHERS (DEGREES): NULL ; NULL ; NULL REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 366 ; 6.312 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 138 ;32.814 ;22.464 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 521 ;16.312 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 30 ;21.220 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 437 ; 0.158 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 2288 ; 0.011 ; 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): 1822 ; 1.363 ; 1.500 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 2923 ; 2.292 ; 2.000 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 1163 ; 3.434 ; 3.000 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 1101 ; 5.372 ; 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: HYDROGENS HAVE BEEN ADDED IN THE RIDING REMARK 3 POSITIONS REMARK 4 REMARK 4 3A04 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 04-MAR-09. REMARK 100 THE DEPOSITION ID IS D_1000028643. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 01-JAN-08 REMARK 200 TEMPERATURE (KELVIN) : 95 REMARK 200 PH : 6.6 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-5A REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.0000 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 315 REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : HKL-2000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 35319 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.970 REMARK 200 RESOLUTION RANGE LOW (A) : 50.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.1 REMARK 200 DATA REDUNDANCY : 13.80 REMARK 200 R MERGE (I) : 0.06000 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 72.6000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.97 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.04 REMARK 200 COMPLETENESS FOR SHELL (%) : 93.8 REMARK 200 DATA REDUNDANCY IN SHELL : 9.80 REMARK 200 R MERGE FOR SHELL (I) : 0.25900 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 7.000 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: MOLREP REMARK 200 STARTING MODEL: PDB ENTRY 3A04 REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 58.30 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.95 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 100MM IMIDAZOLE (PH6.6), 5% PEG6000, REMARK 280 5MM CADMIUM CHLORIDE, VAPOR DIFFUSION, SITTING DROP, TEMPERATURE REMARK 280 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 48.90300 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 48.90300 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 49.35450 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 51.59700 REMARK 290 SMTRY3 5 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 6 -1.000000 0.000000 0.000000 49.35450 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 51.59700 REMARK 290 SMTRY3 6 0.000000 0.000000 1.000000 48.90300 REMARK 290 SMTRY1 7 -1.000000 0.000000 0.000000 49.35450 REMARK 290 SMTRY2 7 0.000000 1.000000 0.000000 51.59700 REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 48.90300 REMARK 290 SMTRY1 8 1.000000 0.000000 0.000000 49.35450 REMARK 290 SMTRY2 8 0.000000 -1.000000 0.000000 51.59700 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: 4390 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 30060 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -86.0 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 -98.70900 REMARK 350 BIOMT2 2 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT3 2 0.000000 0.000000 -1.000000 -48.90300 REMARK 375 REMARK 375 SPECIAL POSITION REMARK 375 THE FOLLOWING ATOMS ARE FOUND TO BE WITHIN 0.15 ANGSTROMS REMARK 375 OF A SYMMETRY RELATED ATOM AND ARE ASSUMED TO BE ON SPECIAL REMARK 375 POSITIONS. REMARK 375 REMARK 375 ATOM RES CSSEQI REMARK 375 CE MET A 186 LIES ON A SPECIAL POSITION. REMARK 375 HOH A 704 LIES ON A SPECIAL POSITION. 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 ALA A 2 REMARK 465 ALA A 3 REMARK 465 GLU A 4 REMARK 465 ARG A 5 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 LEU A 6 CG CD1 CD2 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 NH2 ARG A 126 OE1 GLU A 130 1.89 REMARK 500 OE2 GLU A 319 O HOH A 566 2.07 REMARK 500 O HOH A 646 O HOH A 647 2.10 REMARK 500 O HOH A 507 O HOH A 537 2.12 REMARK 500 O HOH A 637 O HOH A 638 2.13 REMARK 500 O HOH A 657 O HOH A 658 2.15 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 OE1 GLU A 69 CD CD A 374 8445 1.44 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 239 CD GLU A 239 OE2 0.077 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 159 CB - CA - C ANGL. DEV. = -13.5 DEGREES REMARK 500 PHE A 159 N - CA - CB ANGL. DEV. = 28.3 DEGREES REMARK 500 LEU A 181 CB - CG - CD1 ANGL. DEV. = -11.4 DEGREES REMARK 500 ARG A 226 NE - CZ - NH1 ANGL. DEV. = 3.2 DEGREES REMARK 500 MET A 232 CG - SD - CE ANGL. DEV. = -11.9 DEGREES REMARK 500 MET A 257 CA - CB - CG ANGL. DEV. = 13.0 DEGREES REMARK 500 LEU A 268 CA - CB - CG ANGL. DEV. = -14.4 DEGREES REMARK 500 GLU A 343 OE1 - CD - OE2 ANGL. DEV. = -7.6 DEGREES REMARK 500 ARG A 347 NE - CZ - NH2 ANGL. DEV. = 3.6 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 7 76.65 -112.15 REMARK 500 TYR A 132 -64.46 -95.40 REMARK 500 ASN A 153 38.44 -141.11 REMARK 500 LYS A 256 134.13 -34.88 REMARK 500 ARG A 261 74.71 -116.49 REMARK 500 HIS A 312 -54.31 -139.51 REMARK 500 REMARK 500 REMARK: NULL REMARK 620 REMARK 620 METAL COORDINATION REMARK 620 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 620 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE): REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 SF4 A 373 FE4 REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS A 303 SG REMARK 620 2 SF4 A 373 S1 115.9 REMARK 620 3 SF4 A 373 S2 100.9 104.7 REMARK 620 4 SF4 A 373 S3 123.2 102.7 107.9 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 CD A 375 CD REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HIS A 307 NE2 REMARK 620 2 HOH A 584 O 100.6 REMARK 620 3 HOH A 653 O 88.7 102.7 REMARK 620 N 1 2 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 SF4 A 373 FE2 REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS A 327 SG REMARK 620 2 SF4 A 373 S1 113.7 REMARK 620 3 SF4 A 373 S3 116.7 103.1 REMARK 620 4 SF4 A 373 S4 111.7 104.8 105.8 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 SF4 A 373 FE3 REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS A 334 SG REMARK 620 2 SF4 A 373 S1 110.4 REMARK 620 3 SF4 A 373 S2 109.9 106.3 REMARK 620 4 SF4 A 373 S4 121.4 102.7 105.0 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 SF4 A 373 FE1 REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS A 337 SG REMARK 620 2 SF4 A 373 S2 110.2 REMARK 620 3 SF4 A 373 S3 116.2 106.4 REMARK 620 4 SF4 A 373 S4 112.8 105.4 105.1 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 CD A 374 CD REMARK 620 N RES CSSEQI ATOM REMARK 620 1 GLU A 343 OE1 REMARK 620 2 GLU A 343 OE2 49.0 REMARK 620 3 GLU A 346 OE1 91.0 138.2 REMARK 620 N 1 2 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SF4 A 373 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CD A 374 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CD A 375 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 3A05 RELATED DB: PDB DBREF 3A04 A 1 372 UNP Q9Y924 SYW_AERPE 1 372 SEQRES 1 A 372 MET ALA ALA GLU ARG LEU ASP PRO TRP GLY ALA VAL GLU SEQRES 2 A 372 ILE LYS ASP TYR ASP ARG LEU LEU ARG THR PHE GLY ILE SEQRES 3 A 372 ARG PRO PHE SER GLU VAL LEU PRO LEU LEU ARG LYS ALA SEQRES 4 A 372 GLY MET GLU PRO SER PHE LEU MET ARG ARG GLY ILE ILE SEQRES 5 A 372 PHE GLY HIS ARG ASP PHE ASP LYS ILE LEU GLU ALA LYS SEQRES 6 A 372 ALA ARG GLY GLU ARG VAL ALA VAL LEU THR GLY PHE MET SEQRES 7 A 372 PRO SER GLY LYS PHE HIS PHE GLY HIS LYS LEU THR VAL SEQRES 8 A 372 ASP GLN LEU ILE TYR LEU GLN LYS ASN GLY PHE LYS VAL SEQRES 9 A 372 PHE VAL ALA ILE ALA ASP ALA GLU ALA PHE ALA VAL ARG SEQRES 10 A 372 ARG ILE GLY ARG GLU GLU ALA VAL ARG ILE ALA VAL GLU SEQRES 11 A 372 GLU TYR ILE ALA ASN MET ILE ALA LEU GLY LEU ASP PRO SEQRES 12 A 372 LYS ASP THR GLU PHE TYR PHE GLN THR ASN ARG GLY THR SEQRES 13 A 372 PRO TYR PHE ARG LEU ILE GLN LEU PHE SER GLY LYS VAL SEQRES 14 A 372 THR ALA ALA GLU MET GLU ALA ILE TYR GLY GLU LEU THR SEQRES 15 A 372 PRO ALA LYS MET MET ALA SER LEU THR GLN ALA ALA ASP SEQRES 16 A 372 ILE LEU HIS VAL GLN LEU ASP GLU TYR GLY GLY TYR ARG SEQRES 17 A 372 HIS VAL VAL VAL PRO VAL GLY ALA ASP GLN ASP PRO HIS SEQRES 18 A 372 LEU ARG LEU THR ARG ASP LEU ALA ASP ARG MET ALA GLY SEQRES 19 A 372 VAL VAL GLU LEU GLU ARG PRO ALA SER THR TYR HIS LYS SEQRES 20 A 372 LEU GLN PRO GLY LEU ASP GLY ARG LYS MET SER SER SER SEQRES 21 A 372 ARG PRO ASP SER THR ILE PHE LEU THR ASP PRO PRO GLU SEQRES 22 A 372 VAL ALA ARG ASN LYS LEU PHE ARG ALA LEU THR GLY GLY SEQRES 23 A 372 ARG ALA THR ALA GLU GLU GLN ARG ARG LEU GLY GLY VAL SEQRES 24 A 372 PRO GLU VAL CYS SER VAL TYR HIS MET ASP LEU TYR HIS SEQRES 25 A 372 LEU MET PRO ASP ASP GLY GLU VAL LYS HIS ILE TYR THR SEQRES 26 A 372 SER CYS ARG LEU GLY LYS ILE LEU CYS GLY GLU CYS LYS SEQRES 27 A 372 GLN ILE ALA TRP GLU LYS LEU GLU ARG PHE LEU ALA GLU SEQRES 28 A 372 HIS GLN SER ARG LEU GLU LYS ALA LYS THR ILE ALA TRP SEQRES 29 A 372 LYS LEU VAL GLU PRO PRO ARG PHE HET SF4 A 373 8 HET CD A 374 1 HET CD A 375 1 HETNAM SF4 IRON/SULFUR CLUSTER HETNAM CD CADMIUM ION FORMUL 2 SF4 FE4 S4 FORMUL 3 CD 2(CD 2+) FORMUL 5 HOH *329(H2 O) HELIX 1 1 TYR A 17 THR A 23 1 7 HELIX 2 2 VAL A 32 ALA A 39 1 8 HELIX 3 3 SER A 44 ARG A 49 1 6 HELIX 4 4 ASP A 57 ARG A 67 1 11 HELIX 5 5 HIS A 84 ASN A 100 1 17 HELIX 6 6 ALA A 109 VAL A 116 1 8 HELIX 7 7 GLY A 120 GLU A 131 1 12 HELIX 8 8 TYR A 132 GLY A 140 1 9 HELIX 9 9 THR A 152 ARG A 154 5 3 HELIX 10 10 GLY A 155 SER A 166 1 12 HELIX 11 11 THR A 170 GLY A 179 1 10 HELIX 12 12 THR A 182 HIS A 198 1 17 HELIX 13 13 VAL A 199 GLY A 205 5 7 HELIX 14 14 GLN A 218 MET A 232 1 15 HELIX 15 15 ARG A 261 THR A 265 5 5 HELIX 16 16 PRO A 271 ARG A 281 1 11 HELIX 17 17 THR A 289 GLY A 297 1 9 HELIX 18 18 VAL A 299 VAL A 302 5 4 HELIX 19 19 CYS A 303 HIS A 312 1 10 HELIX 20 20 ASP A 316 LEU A 329 1 14 HELIX 21 21 LEU A 333 LYS A 365 1 33 SHEET 1 A 7 ARG A 27 PRO A 28 0 SHEET 2 A 7 ILE A 52 ARG A 56 -1 O HIS A 55 N ARG A 27 SHEET 3 A 7 ALA A 242 HIS A 246 -1 O TYR A 245 N GLY A 54 SHEET 4 A 7 VAL A 210 GLY A 215 1 N VAL A 214 O THR A 244 SHEET 5 A 7 ALA A 72 PHE A 77 1 N ALA A 72 O VAL A 211 SHEET 6 A 7 LYS A 103 ILE A 108 1 O ALA A 107 N THR A 75 SHEET 7 A 7 GLU A 147 PHE A 150 1 O TYR A 149 N ILE A 108 LINK SG CYS A 303 FE4 SF4 A 373 1555 1555 2.35 LINK NE2 HIS A 307 CD CD A 375 1555 1555 2.48 LINK SG CYS A 327 FE2 SF4 A 373 1555 1555 2.23 LINK SG CYS A 334 FE3 SF4 A 373 1555 1555 2.27 LINK SG CYS A 337 FE1 SF4 A 373 1555 1555 2.28 LINK OE1 GLU A 343 CD CD A 374 1555 1555 2.23 LINK OE2 GLU A 343 CD CD A 374 1555 1555 2.62 LINK OE1 GLU A 346 CD CD A 374 1555 1555 2.35 LINK CD CD A 375 O HOH A 584 1555 1555 2.64 LINK CD CD A 375 O HOH A 653 1555 1555 2.02 SITE 1 AC1 7 GLY A 285 GLY A 286 CYS A 303 CYS A 327 SITE 2 AC1 7 ILE A 332 CYS A 334 CYS A 337 SITE 1 AC2 4 GLU A 69 HIS A 209 GLU A 343 GLU A 346 SITE 1 AC3 4 GLU A 13 HIS A 307 HOH A 584 HOH A 653 CRYST1 98.709 103.194 97.806 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 0.010131 0.000000 0.000000 0.00000 SCALE2 0.000000 0.009690 0.000000 0.00000 SCALE3 0.000000 0.000000 0.010224 0.00000