PDB Short entry for 1X54 HEADER LIGASE 15-MAY-05 1X54 TITLE CRYSTAL STRUCTURE OF ASPARAGINYL-TRNA SYNTHETASE FROM PYROCOCCUS TITLE 2 HORIKOSHII COMPLEXED WITH ASPARAGINYL-ADENYLATE COMPND MOL_ID: 1; COMPND 2 MOLECULE: ASPARAGINYL-TRNA SYNTHETASE; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: ASPARAGINE-TRNA LIGASE, ASNRS; COMPND 5 EC: 6.1.1.22; COMPND 6 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: PYROCOCCUS HORIKOSHII; SOURCE 3 ORGANISM_TAXID: 53953; SOURCE 4 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 5 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 6 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 7 EXPRESSION_SYSTEM_PLASMID: PET11A KEYWDS AMINOACYL-TRNA SYNTHETASE, RIKEN STRUCTURAL GENOMICS/PROTEOMICS KEYWDS 2 INITIATIVE, RSGI, STRUCTURAL GENOMICS, LIGASE EXPDTA X-RAY DIFFRACTION AUTHOR W.IWASAKI,S.SEKINE,S.YOKOYAMA,RIKEN STRUCTURAL GENOMICS/PROTEOMICS AUTHOR 2 INITIATIVE (RSGI) REVDAT 5 25-OCT-23 1X54 1 REMARK LINK REVDAT 4 13-JUL-11 1X54 1 VERSN REVDAT 3 24-FEB-09 1X54 1 VERSN REVDAT 2 18-JUL-06 1X54 1 JRNL REVDAT 1 23-MAY-06 1X54 0 JRNL AUTH W.IWASAKI,S.SEKINE,C.KUROISHI,S.KURAMITSU,M.SHIROUZU, JRNL AUTH 2 S.YOKOYAMA JRNL TITL STRUCTURAL BASIS OF THE WATER-ASSISTED ASPARAGINE JRNL TITL 2 RECOGNITION BY ASPARAGINYL-TRNA SYNTHETASE. JRNL REF J.MOL.BIOL. V. 360 329 2006 JRNL REFN ISSN 0022-2836 JRNL PMID 16753178 JRNL DOI 10.1016/J.JMB.2006.04.068 REMARK 2 REMARK 2 RESOLUTION. 1.45 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.1.9999 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) : 1.45 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 30.29 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : NULL REMARK 3 NUMBER OF REFLECTIONS : 92348 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) : 0.169 REMARK 3 R VALUE (WORKING SET) : 0.168 REMARK 3 FREE R VALUE : 0.192 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.000 REMARK 3 FREE R VALUE TEST SET COUNT : 4882 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) : 1.45 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.49 REMARK 3 REFLECTION IN BIN (WORKING SET) : 5425 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : NULL REMARK 3 BIN R VALUE (WORKING SET) : 0.2040 REMARK 3 BIN FREE R VALUE SET COUNT : 263 REMARK 3 BIN FREE R VALUE : 0.2380 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 3544 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 40 REMARK 3 SOLVENT ATOMS : 309 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 21.34 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -0.03000 REMARK 3 B22 (A**2) : 0.11000 REMARK 3 B33 (A**2) : -0.12000 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : -0.04000 REMARK 3 B23 (A**2) : 0.00000 REMARK 3 REMARK 3 ESTIMATED OVERALL COORDINATE ERROR. REMARK 3 ESU BASED ON R VALUE (A): 0.065 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.058 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.035 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 1.942 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.969 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.958 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 3674 ; 0.010 ; 0.022 REMARK 3 BOND LENGTHS OTHERS (A): NULL ; NULL ; NULL REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 4977 ; 1.296 ; 1.966 REMARK 3 BOND ANGLES OTHERS (DEGREES): NULL ; NULL ; NULL REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 431 ; 5.823 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 172 ;33.413 ;23.605 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 652 ;12.746 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 27 ;12.828 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 531 ; 0.091 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 2767 ; 0.006 ; 0.020 REMARK 3 GENERAL PLANES OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): 1572 ; 0.196 ; 0.200 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): 287 ; 0.130 ; 0.200 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): 91 ; 0.140 ; 0.200 REMARK 3 SYMMETRY VDW OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY H-BOND REFINED ATOMS (A): 43 ; 0.134 ; 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): 2238 ; 1.205 ; 1.500 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 3507 ; 1.721 ; 2.000 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 1673 ; 3.686 ; 3.000 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 1470 ; 3.799 ; 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): 3911 ; 3.911 ; 3.000 REMARK 3 SPHERICITY; FREE ATOMS (A**2): 310 ; 4.605 ; 3.000 REMARK 3 SPHERICITY; BONDED ATOMS (A**2): 3583 ; 3.362 ; 3.000 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 : 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: NULL REMARK 4 REMARK 4 1X54 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 19-MAY-05. REMARK 100 THE DEPOSITION ID IS D_1000024390. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 15-DEC-04 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 : SPRING-8 REMARK 200 BEAMLINE : BL41XU REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.0 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 : SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 97438 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.450 REMARK 200 RESOLUTION RANGE LOW (A) : 50.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : -3.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 96.1 REMARK 200 DATA REDUNDANCY : 4.300 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : NULL REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.45 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.50 REMARK 200 COMPLETENESS FOR SHELL (%) : 78.1 REMARK 200 DATA REDUNDANCY IN SHELL : 3.50 REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 <I/SIGMA(I)> FOR SHELL : NULL REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: MOLREP REMARK 200 STARTING MODEL: PDB ENTRY 1B8A REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 57.10 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.90 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: PEG8000, PH 6.5, VAPOR DIFFUSION, REMARK 280 SITTING DROP, TEMPERATURE 293K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: C 1 2 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,Y,-Z REMARK 290 3555 X+1/2,Y+1/2,Z REMARK 290 4555 -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 0.00000 REMARK 290 SMTRY1 3 1.000000 0.000000 0.000000 63.03550 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 34.11050 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 4 -1.000000 0.000000 0.000000 63.03550 REMARK 290 SMTRY2 4 0.000000 1.000000 0.000000 34.11050 REMARK 290 SMTRY3 4 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 300 REMARK: THE SECOND PART OF THE BIOLOGICAL ASSEMBLY IS GENERATED REMARK 300 BY THE TWO FOLD AXIS: -X, Y, -Z. 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,PQS REMARK 350 TOTAL BURIED SURFACE AREA: 10900 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 33160 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -92.0 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 -34.58155 REMARK 350 BIOMT2 2 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT3 2 0.000000 0.000000 -1.000000 67.34623 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 A1053 LIES ON A SPECIAL POSITION. REMARK 375 HOH A1413 LIES ON A SPECIAL POSITION. REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CLOSE CONTACTS IN SAME ASYMMETRIC UNIT REMARK 500 REMARK 500 THE FOLLOWING ATOMS ARE IN CLOSE CONTACT. REMARK 500 REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI DISTANCE REMARK 500 O HOH A 1126 O HOH A 1708 2.07 REMARK 500 O HOH A 1119 O HOH A 1709 2.08 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 ASP A 81 CB - CG - OD2 ANGL. DEV. = 6.0 DEGREES REMARK 500 ASP A 120 CB - CG - OD2 ANGL. DEV. = 6.5 DEGREES REMARK 500 ASP A 337 CB - CG - OD2 ANGL. DEV. = 6.1 DEGREES REMARK 500 ASP A 340 CB - CG - OD2 ANGL. DEV. = 6.2 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 PHE A 179 -115.01 53.41 REMARK 500 SER A 188 140.51 178.55 REMARK 500 GLU A 201 -53.61 68.29 REMARK 500 TRP A 233 -20.02 78.25 REMARK 500 ASP A 340 88.97 -150.17 REMARK 500 TYR A 394 54.61 -114.87 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 MG A2000 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 GLU A 357 OE1 REMARK 620 2 HOH A1074 O 93.2 REMARK 620 3 HOH A1702 O 93.4 84.4 REMARK 620 4 HOH A1703 O 85.5 97.4 177.9 REMARK 620 5 HOH A1705 O 179.6 86.4 86.4 94.7 REMARK 620 6 4AD A2001 O2P 89.7 175.1 91.5 86.7 90.7 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 MG A 2000 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE 4AD A 2001 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MPD A 2002 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 1X55 RELATED DB: PDB REMARK 900 RELATED ID: 1X56 RELATED DB: PDB REMARK 900 RELATED ID: PHO001000241.3 RELATED DB: TARGETDB DBREF 1X54 A 1 434 UNP O57980 SYN_PYRHO 1 434 SEQRES 1 A 434 MET ILE GLU LYS VAL TYR CYS GLN GLU VAL LYS PRO GLU SEQRES 2 A 434 LEU ASP GLY LYS LYS VAL ARG LEU ALA GLY TRP VAL TYR SEQRES 3 A 434 THR ASN MET ARG VAL GLY LYS LYS ILE PHE LEU TRP ILE SEQRES 4 A 434 ARG ASP SER THR GLY ILE VAL GLN ALA VAL VAL ALA LYS SEQRES 5 A 434 ASN VAL VAL GLY GLU GLU THR PHE GLU LYS ALA LYS LYS SEQRES 6 A 434 LEU GLY ARG GLU SER SER VAL ILE VAL GLU GLY ILE VAL SEQRES 7 A 434 LYS ALA ASP GLU ARG ALA PRO GLY GLY ALA GLU VAL HIS SEQRES 8 A 434 VAL GLU LYS LEU GLU VAL ILE GLN ALA VAL SER GLU PHE SEQRES 9 A 434 PRO ILE PRO GLU ASN PRO GLU GLN ALA SER PRO GLU LEU SEQRES 10 A 434 LEU LEU ASP TYR ARG HIS LEU HIS ILE ARG THR PRO LYS SEQRES 11 A 434 ALA SER ALA ILE MET LYS VAL LYS GLU THR LEU ILE MET SEQRES 12 A 434 ALA ALA ARG GLU TRP LEU LEU LYS ASP GLY TRP HIS GLU SEQRES 13 A 434 VAL PHE PRO PRO ILE LEU VAL THR GLY ALA VAL GLU GLY SEQRES 14 A 434 GLY ALA THR LEU PHE LYS LEU LYS TYR PHE ASP LYS TYR SEQRES 15 A 434 ALA TYR LEU SER GLN SER ALA GLN LEU TYR LEU GLU ALA SEQRES 16 A 434 ALA ILE PHE GLY LEU GLU LYS VAL TRP SER LEU THR PRO SEQRES 17 A 434 SER PHE ARG ALA GLU LYS SER ARG THR ARG ARG HIS LEU SEQRES 18 A 434 THR GLU PHE TRP HIS LEU GLU LEU GLU ALA ALA TRP MET SEQRES 19 A 434 ASP LEU TRP ASP ILE MET LYS VAL GLU GLU GLU LEU VAL SEQRES 20 A 434 SER TYR MET VAL GLN ARG THR LEU GLU LEU ARG LYS LYS SEQRES 21 A 434 GLU ILE GLU MET PHE ARG ASP ASP LEU THR THR LEU LYS SEQRES 22 A 434 ASN THR GLU PRO PRO PHE PRO ARG ILE SER TYR ASP GLU SEQRES 23 A 434 ALA ILE ASP ILE LEU GLN SER LYS GLY VAL ASN VAL GLU SEQRES 24 A 434 TRP GLY ASP ASP LEU GLY ALA ASP GLU GLU ARG VAL LEU SEQRES 25 A 434 THR GLU GLU PHE ASP ARG PRO PHE PHE VAL TYR GLY TYR SEQRES 26 A 434 PRO LYS HIS ILE LYS ALA PHE TYR MET LYS GLU ASP PRO SEQRES 27 A 434 ASN ASP PRO ARG LYS VAL LEU ALA SER ASP MET LEU ALA SEQRES 28 A 434 PRO GLU GLY TYR GLY GLU ILE ILE GLY GLY SER GLN ARG SEQRES 29 A 434 GLU ASP ASP TYR ASP LYS LEU LEU ASN ARG ILE LEU GLU SEQRES 30 A 434 GLU GLY MET ASP PRO LYS ASP TYR GLU TRP TYR LEU ASP SEQRES 31 A 434 LEU ARG ARG TYR GLY SER VAL PRO HIS SER GLY PHE GLY SEQRES 32 A 434 LEU GLY VAL GLU ARG LEU VAL ALA TRP VAL LEU LYS LEU SEQRES 33 A 434 ASP HIS ILE ARG TRP ALA ALA LEU PHE PRO ARG THR PRO SEQRES 34 A 434 ALA ARG LEU TYR PRO HET MG A2000 1 HET 4AD A2001 31 HET MPD A2002 8 HETNAM MG MAGNESIUM ION HETNAM 4AD 4-AMINO-1,4-DIOXOBUTAN-2-AMINIUM ADENOSINE-5'- HETNAM 2 4AD MONOPHOSPHATE HETNAM MPD (4S)-2-METHYL-2,4-PENTANEDIOL HETSYN 4AD ASNAMP FORMUL 2 MG MG 2+ FORMUL 3 4AD C14 H21 N7 O9 P 1+ FORMUL 4 MPD C6 H14 O2 FORMUL 5 HOH *309(H2 O) HELIX 1 1 TYR A 6 VAL A 10 5 5 HELIX 2 2 LYS A 11 ASP A 15 5 5 HELIX 3 3 ALA A 51 GLY A 56 1 6 HELIX 4 4 GLY A 56 LYS A 65 1 10 HELIX 5 5 ALA A 84 GLY A 86 5 3 HELIX 6 6 ASN A 109 ALA A 113 5 5 HELIX 7 7 SER A 114 TYR A 121 1 8 HELIX 8 8 TYR A 121 ILE A 126 1 6 HELIX 9 9 THR A 128 ASP A 152 1 25 HELIX 10 10 GLY A 169 LEU A 173 5 5 HELIX 11 11 ALA A 189 GLU A 201 1 13 HELIX 12 12 ASP A 235 ARG A 258 1 24 HELIX 13 13 ARG A 258 MET A 264 1 7 HELIX 14 14 LEU A 269 ASN A 274 1 6 HELIX 15 15 TYR A 284 LYS A 294 1 11 HELIX 16 16 GLY A 305 GLU A 314 1 10 HELIX 17 17 HIS A 328 LYS A 330 5 3 HELIX 18 18 ASP A 367 GLU A 378 1 12 HELIX 19 19 ASP A 381 ASP A 384 5 4 HELIX 20 20 TYR A 385 LEU A 391 1 7 HELIX 21 21 VAL A 406 LEU A 414 1 9 HELIX 22 22 HIS A 418 ALA A 423 5 6 SHEET 1 A 6 LYS A 18 VAL A 31 0 SHEET 2 A 6 LYS A 34 ASP A 41 -1 O TRP A 38 N TYR A 26 SHEET 3 A 6 GLY A 44 VAL A 50 -1 O VAL A 50 N ILE A 35 SHEET 4 A 6 ALA A 88 GLN A 99 1 O VAL A 90 N VAL A 49 SHEET 5 A 6 SER A 71 ALA A 80 -1 N ILE A 77 O HIS A 91 SHEET 6 A 6 LYS A 18 VAL A 31 -1 N LEU A 21 O VAL A 74 SHEET 1 B 8 HIS A 155 GLU A 156 0 SHEET 2 B 8 LYS A 202 PHE A 210 1 O LYS A 202 N HIS A 155 SHEET 3 B 8 GLU A 223 ALA A 232 -1 O PHE A 224 N SER A 209 SHEET 4 B 8 HIS A 399 GLY A 405 -1 O LEU A 404 N LEU A 227 SHEET 5 B 8 GLY A 356 GLN A 363 -1 N GLY A 360 O GLY A 403 SHEET 6 B 8 LYS A 343 ALA A 351 -1 N MET A 349 O ILE A 358 SHEET 7 B 8 PHE A 320 PRO A 326 -1 N PHE A 320 O LEU A 350 SHEET 8 B 8 ARG A 281 SER A 283 1 N ILE A 282 O PHE A 321 SHEET 1 C 3 LEU A 162 VAL A 163 0 SHEET 2 C 3 LYS A 181 LEU A 185 -1 O TYR A 184 N VAL A 163 SHEET 3 C 3 LYS A 175 TYR A 178 -1 N TYR A 178 O LYS A 181 LINK OE1 GLU A 357 MG MG A2000 1555 1555 2.21 LINK O HOH A1074 MG MG A2000 1555 1555 2.34 LINK O HOH A1702 MG MG A2000 1555 1555 2.11 LINK O HOH A1703 MG MG A2000 1555 1555 2.22 LINK O HOH A1705 MG MG A2000 1555 1555 2.22 LINK MG MG A2000 O2P 4AD A2001 1555 1555 2.08 CISPEP 1 PRO A 277 PRO A 278 0 1.71 CISPEP 2 TYR A 433 PRO A 434 0 -1.21 SITE 1 AC1 6 GLU A 357 HOH A1074 HOH A1702 HOH A1703 SITE 2 AC1 6 HOH A1705 4AD A2001 SITE 1 AC2 27 GLU A 168 SER A 188 GLN A 190 ARG A 211 SITE 2 AC2 27 HIS A 220 LEU A 221 PHE A 224 HIS A 226 SITE 3 AC2 27 GLU A 228 TYR A 333 GLU A 357 ILE A 358 SITE 4 AC2 27 ILE A 359 GLY A 360 ARG A 364 PHE A 402 SITE 5 AC2 27 GLY A 403 GLY A 405 ARG A 408 HOH A1003 SITE 6 AC2 27 HOH A1008 HOH A1014 HOH A1373 HOH A1702 SITE 7 AC2 27 HOH A1703 HOH A1705 MG A2000 SITE 1 AC3 4 ILE A 98 ASP A 366 SER A 396 HOH A1058 CRYST1 126.071 68.221 75.706 90.00 117.18 90.00 C 1 2 1 4 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 0.007932 0.000000 0.004074 0.00000 SCALE2 0.000000 0.014658 0.000000 0.00000 SCALE3 0.000000 0.000000 0.014849 0.00000