HEADER LIGASE 07-JUN-09 3A31 TITLE CRYSTAL STRUCTURE OF PUTATIVE THREONYL-TRNA SYNTHETASE THRRS-1 FROM TITLE 2 AEROPYRUM PERNIX (SELENOMETHIONINE DERIVATIVE) COMPND MOL_ID: 1; COMPND 2 MOLECULE: PROBABLE THREONYL-TRNA SYNTHETASE 1; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: THREONINE--TRNA LIGASE 1, THRRS 1; COMPND 5 EC: 6.1.1.3; COMPND 6 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: AEROPYRUM PERNIX; SOURCE 3 ORGANISM_TAXID: 56636; SOURCE 4 STRAIN: AEROPYRUM PERNIX K1; SOURCE 5 GENE: APE0809.1; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 8 EXPRESSION_SYSTEM_STRAIN: DE3; SOURCE 9 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 10 EXPRESSION_SYSTEM_PLASMID: PE11A KEYWDS THREONYL-TRNA SYNTHETASE, AEROPYRUM PERNIX K1, PROTEIN BIOSYNTHESIS, KEYWDS 2 AMINOACYL-TRNA SYNTHETASE, ATP-BINDING, LIGASE, METAL-BINDING, KEYWDS 3 NUCLEOTIDE-BINDING EXPDTA X-RAY DIFFRACTION AUTHOR S.SHIMIZU,E.C.M.JUAN,Y.MIYASHITA,Y.SATO,M.M.HOQUE,K.SUZUKI, AUTHOR 2 M.YOGIASHI,M.TSUNODA,A.-C.DOCK-BREGEON,D.MORAS,T.SEKIGUCHI, AUTHOR 3 A.TAKENAKA REVDAT 3 20-NOV-24 3A31 1 REMARK LINK REVDAT 2 20-NOV-13 3A31 1 JRNL VERSN REVDAT 1 27-OCT-09 3A31 0 JRNL AUTH S.SHIMIZU,E.C.M.JUAN,Y.SATO,Y.MIYASHITA,M.M.HOQUE,K.SUZUKI, JRNL AUTH 2 T.SAGARA,M.TSUNODA,T.SEKIGUCHI,A.-C.DOCK-BREGEON,D.MORAS, JRNL AUTH 3 A.TAKENAKA JRNL TITL TWO COMPLEMENTARY ENZYMES FOR THREONYLATION OF TRNA IN JRNL TITL 2 CRENARCHAEOTA: CRYSTAL STRUCTURE OF AEROPYRUM PERNIX JRNL TITL 3 THREONYL-TRNA SYNTHETASE LACKING A CIS-EDITING DOMAIN JRNL REF J.MOL.BIOL. V. 394 286 2009 JRNL REFN ISSN 0022-2836 JRNL PMID 19761773 JRNL DOI 10.1016/J.JMB.2009.09.018 REMARK 2 REMARK 2 RESOLUTION. 2.50 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.2.0019 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) : 2.50 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 41.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 100.0 REMARK 3 NUMBER OF REFLECTIONS : 16983 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) : 0.170 REMARK 3 R VALUE (WORKING SET) : 0.170 REMARK 3 FREE R VALUE : 0.240 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.100 REMARK 3 FREE R VALUE TEST SET COUNT : 859 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) : 2.50 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.57 REMARK 3 REFLECTION IN BIN (WORKING SET) : 1183 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 100.0 REMARK 3 BIN R VALUE (WORKING SET) : 0.1500 REMARK 3 BIN FREE R VALUE SET COUNT : 72 REMARK 3 BIN FREE R VALUE : 0.2600 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 3710 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 11 REMARK 3 SOLVENT ATOMS : 269 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 22.00 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 0.01000 REMARK 3 B22 (A**2) : -0.02000 REMARK 3 B33 (A**2) : 0.02000 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): 2.081 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.263 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.155 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 6.749 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.961 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.927 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 3800 ; 0.021 ; 0.022 REMARK 3 BOND LENGTHS OTHERS (A): NULL ; NULL ; NULL REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 5125 ; 1.956 ; 1.970 REMARK 3 BOND ANGLES OTHERS (DEGREES): NULL ; NULL ; NULL REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 464 ;14.622 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 179 ;32.672 ;22.626 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 665 ;16.161 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 35 ;16.345 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 556 ; 0.129 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 2881 ; 0.008 ; 0.020 REMARK 3 GENERAL PLANES OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): 1648 ; 0.231 ; 0.200 REMARK 3 NON-BONDED CONTACTS OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION REFINED ATOMS (A): 2584 ; 0.317 ; 0.200 REMARK 3 NON-BONDED TORSION OTHERS (A): NULL ; NULL ; NULL REMARK 3 H-BOND (X...Y) REFINED ATOMS (A): 243 ; 0.205 ; 0.200 REMARK 3 H-BOND (X...Y) OTHERS (A): NULL ; NULL ; NULL REMARK 3 POTENTIAL METAL-ION REFINED ATOMS (A): 2 ; 0.039 ; 0.200 REMARK 3 POTENTIAL METAL-ION OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY VDW REFINED ATOMS (A): 81 ; 0.242 ; 0.200 REMARK 3 SYMMETRY VDW OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY H-BOND REFINED ATOMS (A): 19 ; 0.166 ; 0.200 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): 2371 ; 1.315 ; 1.500 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 3715 ; 1.909 ; 2.000 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 1604 ; 3.442 ; 3.000 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 1410 ; 5.341 ; 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 3A31 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 08-JUN-09. REMARK 100 THE DEPOSITION ID IS D_1000028748. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 19-NOV-06 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 7.75 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) : 1.00, 0.97898, 0.97966 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 4 REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : HKL-2000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 17033 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.500 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 (%) : 100.0 REMARK 200 DATA REDUNDANCY : 14.50 REMARK 200 R MERGE (I) : 0.08000 REMARK 200 R SYM (I) : NULL REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 46.5000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.50 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.59 REMARK 200 COMPLETENESS FOR SHELL (%) : 100.0 REMARK 200 DATA REDUNDANCY IN SHELL : 14.70 REMARK 200 R MERGE FOR SHELL (I) : 0.26800 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 <I/SIGMA(I)> FOR SHELL : 14.20 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: MAD REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MAD REMARK 200 SOFTWARE USED: SHARP REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 44.80 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.23 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 1.5M AMMONIUM SULFATE IN 0.1M HEPES REMARK 280 (PH7.5) BUFFER, PH 7.75, 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 56.35000 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 56.35000 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 41.00000 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 51.85000 REMARK 290 SMTRY3 5 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 6 -1.000000 0.000000 0.000000 41.00000 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 51.85000 REMARK 290 SMTRY3 6 0.000000 0.000000 1.000000 56.35000 REMARK 290 SMTRY1 7 -1.000000 0.000000 0.000000 41.00000 REMARK 290 SMTRY2 7 0.000000 1.000000 0.000000 51.85000 REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 56.35000 REMARK 290 SMTRY1 8 1.000000 0.000000 0.000000 41.00000 REMARK 290 SMTRY2 8 0.000000 -1.000000 0.000000 51.85000 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: 8700 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 34170 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -171.0 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 0.00000 REMARK 350 BIOMT2 2 0.000000 -1.000000 0.000000 103.70000 REMARK 350 BIOMT3 2 0.000000 0.000000 -1.000000 112.70000 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 HOH A 614 LIES ON A SPECIAL POSITION. REMARK 375 HOH A 701 LIES ON A SPECIAL POSITION. REMARK 375 HOH A 702 LIES ON A SPECIAL POSITION. REMARK 375 HOH A 735 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 MSE A 1 REMARK 465 ALA A 2 REMARK 465 SER A 3 REMARK 465 GLY A 4 REMARK 465 GLN A 5 REMARK 465 ASP A 6 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 101 N - CA - C ANGL. DEV. = -32.2 DEGREES REMARK 500 ARG A 158 NE - CZ - NH2 ANGL. DEV. = -3.2 DEGREES REMARK 500 ASP A 176 CB - CG - OD1 ANGL. DEV. = 5.9 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 VAL A 28 -48.26 65.48 REMARK 500 ASN A 30 66.47 26.01 REMARK 500 SER A 45 -162.72 -109.01 REMARK 500 GLU A 101 54.92 134.57 REMARK 500 ARG A 127 -126.53 37.86 REMARK 500 LYS A 216 -89.79 -123.64 REMARK 500 GLU A 269 -109.87 -58.66 REMARK 500 SER A 270 32.00 118.29 REMARK 500 MSE A 278 -131.05 -116.77 REMARK 500 THR A 394 -70.06 -133.59 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 ILE A 100 GLU A 101 83.67 REMARK 500 GLU A 269 SER A 270 -56.40 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 ZN A 743 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS A 112 SG REMARK 620 2 HIS A 166 NE2 111.4 REMARK 620 3 HIS A 310 ND1 110.1 101.8 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 SO4 A 472 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SO4 A 473 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ZN A 743 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 3A32 RELATED DB: PDB DBREF 3A31 A 1 471 UNP Q9YDW0 SYT1_AERPE 1 471 SEQRES 1 A 471 MSE ALA SER GLY GLN ASP LYS THR HIS ILE ASP TYR ALA SEQRES 2 A 471 TYR GLU LEU ASP ILE THR VAL LYS PRO ASP SER ARG VAL SEQRES 3 A 471 PRO VAL PHE ASN ARG GLU PHE ALA THR PHE THR GLY ALA SEQRES 4 A 471 GLY VAL PRO LEU PHE SER LEU GLY GLY GLY PRO ILE ARG SEQRES 5 A 471 TYR ALA LEU ALA GLU VAL LEU ALA LYS PHE HIS ALA ARG SEQRES 6 A 471 ARG GLY TYR TYR VAL VAL GLU THR PRO ILE ILE ALA SER SEQRES 7 A 471 THR GLU LEU PHE LYS VAL SER GLY HIS ILE GLU PHE TYR SEQRES 8 A 471 ARG ASN ASN MSE TYR LEU PHE ASP ILE GLU GLY HIS GLU SEQRES 9 A 471 PHE ALA VAL LYS PRO MSE ASN CYS PRO TYR HIS ILE LEU SEQRES 10 A 471 LEU PHE LEU ASN GLU VAL ALA LYS HIS ARG SER LYS LEU SEQRES 11 A 471 PRO LEU PRO PHE LYS VAL PHE GLU PHE GLY ARG VAL HIS SEQRES 12 A 471 ARG TYR GLU PRO SER GLY SER ILE TYR GLY LEU LEU ARG SEQRES 13 A 471 VAL ARG GLY PHE THR GLN ASP ASP ALA HIS ILE ILE VAL SEQRES 14 A 471 PRO GLY GLY ARG VAL ILE ASP VAL VAL TYR ASP VAL PHE SEQRES 15 A 471 GLU GLU MSE LYS LEU VAL LEU GLU ARG LEU PHE LYS LEU SEQRES 16 A 471 GLY VAL SER SER GLU THR PHE LYS VAL ARG LEU SER MSE SEQRES 17 A 471 SER ASP LYS SER LEU ILE GLY LYS GLU PHE MSE GLY SER SEQRES 18 A 471 LYS GLU GLU TRP GLU GLY ALA GLU GLU ALA LEU ARG GLU SEQRES 19 A 471 ALA ALA SER ARG ILE ASN GLU LYS TYR GLY ILE ASP ILE SEQRES 20 A 471 VAL GLU LEU GLU GLY GLU ALA ALA PHE TYR GLY PRO LYS SEQRES 21 A 471 LEU ASP PHE ILE MSE MSE VAL GLU GLU SER GLY VAL SER SEQRES 22 A 471 LYS GLU TRP GLN MSE GLY THR ILE GLN PHE ASP PHE ASN SEQRES 23 A 471 LEU PRO ARG ARG PHE ARG LEU TYR ASP VAL VAL ARG GLU SEQRES 24 A 471 GLU PHE GLY ILE GLU GLU VAL TYR ILE ILE HIS ARG ALA SEQRES 25 A 471 LEU LEU GLY SER ILE GLU ARG PHE LEU GLY VAL TYR LEU SEQRES 26 A 471 GLU HIS ARG ARG GLY ARG MSE PRO PHE THR LEU ALA PRO SEQRES 27 A 471 ILE GLN PHE ALA VAL ILE ALA VAL LYS THR GLY GLY GLU SEQRES 28 A 471 VAL ASP ARG GLU ILE GLU ASP LEU ALA SER SER ILE ALA SEQRES 29 A 471 LYS GLY LEU LEU ASP LYS GLY PHE ARG VAL ALA VAL LYS SEQRES 30 A 471 GLY SER SER LYS THR GLY LEU SER SER ASP VAL ARG HIS SEQRES 31 A 471 ILE GLU SER THR ALA LYS PRO ALA VAL ASN VAL PHE ILE SEQRES 32 A 471 GLY ALA LYS GLU VAL ARG GLU LYS VAL LEU ASP VAL ARG SEQRES 33 A 471 VAL PHE ASP LEU GLU SER MSE LYS ARG ARG ARG LEU ALA SEQRES 34 A 471 ILE ALA TYR GLY ASP ALA ALA ASP ALA VAL GLU ASN LEU SEQRES 35 A 471 ALA ALA VAL ALA GLU GLU LEU GLU SER PRO VAL ARG SER SEQRES 36 A 471 LEU SER GLY GLN ALA PRO ARG ILE PRO ALA ASP PHE SER SEQRES 37 A 471 PHE MSE LEU MODRES 3A31 MSE A 95 MET SELENOMETHIONINE MODRES 3A31 MSE A 110 MET SELENOMETHIONINE MODRES 3A31 MSE A 185 MET SELENOMETHIONINE MODRES 3A31 MSE A 208 MET SELENOMETHIONINE MODRES 3A31 MSE A 219 MET SELENOMETHIONINE MODRES 3A31 MSE A 265 MET SELENOMETHIONINE MODRES 3A31 MSE A 266 MET SELENOMETHIONINE MODRES 3A31 MSE A 278 MET SELENOMETHIONINE MODRES 3A31 MSE A 332 MET SELENOMETHIONINE MODRES 3A31 MSE A 423 MET SELENOMETHIONINE MODRES 3A31 MSE A 470 MET SELENOMETHIONINE HET MSE A 95 8 HET MSE A 110 8 HET MSE A 185 8 HET MSE A 208 8 HET MSE A 219 8 HET MSE A 265 8 HET MSE A 266 8 HET MSE A 278 8 HET MSE A 332 8 HET MSE A 423 8 HET MSE A 470 8 HET SO4 A 472 5 HET SO4 A 473 5 HET ZN A 743 1 HETNAM MSE SELENOMETHIONINE HETNAM SO4 SULFATE ION HETNAM ZN ZINC ION FORMUL 1 MSE 11(C5 H11 N O2 SE) FORMUL 2 SO4 2(O4 S 2-) FORMUL 4 ZN ZN 2+ FORMUL 5 HOH *269(H2 O) HELIX 1 1 THR A 8 LEU A 16 1 9 HELIX 2 2 PHE A 33 GLY A 38 1 6 HELIX 3 3 GLY A 47 ARG A 66 1 20 HELIX 4 4 THR A 79 GLY A 86 1 8 HELIX 5 5 PHE A 90 MSE A 95 5 6 HELIX 6 6 ASN A 111 ARG A 127 1 17 HELIX 7 7 SER A 128 LEU A 130 5 3 HELIX 8 8 ARG A 173 LEU A 192 1 20 HELIX 9 9 ASP A 210 ILE A 214 5 5 HELIX 10 10 SER A 221 GLY A 244 1 24 HELIX 11 11 ASN A 286 PHE A 291 1 6 HELIX 12 12 ARG A 292 GLY A 302 1 11 HELIX 13 13 ILE A 317 ARG A 328 1 12 HELIX 14 14 PRO A 333 ALA A 337 5 5 HELIX 15 15 VAL A 352 LYS A 370 1 19 HELIX 16 16 GLY A 383 THR A 394 1 12 HELIX 17 17 GLY A 404 LYS A 411 1 8 HELIX 18 18 ASP A 434 GLY A 458 1 25 HELIX 19 19 SER A 468 LEU A 471 5 4 SHEET 1 A 8 TYR A 69 VAL A 70 0 SHEET 2 A 8 PHE A 134 HIS A 143 1 O LYS A 135 N TYR A 69 SHEET 3 A 8 GLY A 159 PRO A 170 -1 O ASP A 164 N GLU A 138 SHEET 4 A 8 VAL A 306 SER A 316 -1 O TYR A 307 N VAL A 169 SHEET 5 A 8 SER A 273 PHE A 283 -1 N GLN A 282 O HIS A 310 SHEET 6 A 8 LYS A 260 GLU A 268 -1 N PHE A 263 O MSE A 278 SHEET 7 A 8 PHE A 202 SER A 207 -1 N SER A 207 O LYS A 260 SHEET 8 A 8 ASP A 246 LEU A 250 1 O VAL A 248 N LEU A 206 SHEET 1 B 3 ILE A 76 SER A 78 0 SHEET 2 B 3 HIS A 103 VAL A 107 -1 O ALA A 106 N ALA A 77 SHEET 3 B 3 LEU A 97 ILE A 100 -1 N PHE A 98 O PHE A 105 SHEET 1 C 6 LYS A 424 ALA A 431 0 SHEET 2 C 6 VAL A 412 ASP A 419 -1 N LEU A 413 O ILE A 430 SHEET 3 C 6 VAL A 399 ILE A 403 -1 N ASN A 400 O ARG A 416 SHEET 4 C 6 PHE A 341 LYS A 347 1 N ILE A 344 O ILE A 403 SHEET 5 C 6 ARG A 373 SER A 380 1 O LYS A 377 N VAL A 343 SHEET 6 C 6 ALA A 465 ASP A 466 1 O ALA A 465 N VAL A 374 LINK C ASN A 94 N MSE A 95 1555 1555 1.32 LINK C MSE A 95 N TYR A 96 1555 1555 1.32 LINK C PRO A 109 N MSE A 110 1555 1555 1.32 LINK C MSE A 110 N ASN A 111 1555 1555 1.34 LINK C GLU A 184 N MSE A 185 1555 1555 1.35 LINK C MSE A 185 N LYS A 186 1555 1555 1.33 LINK C SER A 207 N MSE A 208 1555 1555 1.34 LINK C MSE A 208 N SER A 209 1555 1555 1.33 LINK C PHE A 218 N MSE A 219 1555 1555 1.32 LINK C MSE A 219 N GLY A 220 1555 1555 1.32 LINK C ILE A 264 N MSE A 265 1555 1555 1.32 LINK C MSE A 265 N MSE A 266 1555 1555 1.33 LINK C MSE A 266 N VAL A 267 1555 1555 1.33 LINK C GLN A 277 N MSE A 278 1555 1555 1.35 LINK C MSE A 278 N GLY A 279 1555 1555 1.34 LINK C ARG A 331 N MSE A 332 1555 1555 1.34 LINK C MSE A 332 N PRO A 333 1555 1555 1.35 LINK C SER A 422 N MSE A 423 1555 1555 1.34 LINK C MSE A 423 N LYS A 424 1555 1555 1.34 LINK C PHE A 469 N MSE A 470 1555 1555 1.35 LINK C MSE A 470 N LEU A 471 1555 1555 1.33 LINK SG CYS A 112 ZN ZN A 743 1555 1555 2.40 LINK NE2 HIS A 166 ZN ZN A 743 1555 1555 1.98 LINK ND1 HIS A 310 ZN ZN A 743 1555 1555 1.99 CISPEP 1 GLY A 86 HIS A 87 0 3.47 CISPEP 2 HIS A 87 ILE A 88 0 -1.89 CISPEP 3 LEU A 132 PRO A 133 0 1.89 CISPEP 4 SER A 270 GLY A 271 0 -25.78 SITE 1 AC1 6 LYS A 7 TYR A 12 SER A 393 LYS A 396 SITE 2 AC1 6 HOH A 610 HOH A 685 SITE 1 AC2 3 ARG A 156 LYS A 406 ARG A 427 SITE 1 AC3 3 CYS A 112 HIS A 166 HIS A 310 CRYST1 82.000 103.700 112.700 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 0.012195 0.000000 0.000000 0.00000 SCALE2 0.000000 0.009643 0.000000 0.00000 SCALE3 0.000000 0.000000 0.008873 0.00000