HEADER LIGASE 22-JUN-09 3HXY TITLE CRYSTAL STRUCTURE OF CATALYTIC FRAGMENT OF E. COLI ALARS IN COMPLEX TITLE 2 WITH AMPPCP, ALA-AMP AND PCP CAVEAT 3HXY LIGANDS MDN, ACP ARE IN CLOSE CONTACT COMPND MOL_ID: 1; COMPND 2 MOLECULE: ALANYL-TRNA SYNTHETASE; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: N-TERMINAL CATALYTIC FRAGMENT RESIDUES 2-442; COMPND 5 SYNONYM: ALANINE-TRNA LIGASE, ALARS; COMPND 6 EC: 6.1.1.7; COMPND 7 ENGINEERED: YES; COMPND 8 MUTATION: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: ESCHERICHIA COLI; SOURCE 3 ORGANISM_TAXID: 83333; SOURCE 4 STRAIN: K-12; SOURCE 5 GENE: ALAS, LOVB, B2697, JW2667; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 8 EXPRESSION_SYSTEM_STRAIN: BL21(DE3) CONDONPLUS; SOURCE 9 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 10 EXPRESSION_SYSTEM_PLASMID: PET20B+ KEYWDS AMINOACYL-TRNA SYNTHETASE, LIGASE, PROTEIN BIOSYNTHESIS, NUCLEOTIDE- KEYWDS 2 BINDING, AMINO ACID-BINDING, ATP-BINDING, METAL-BINDING, ZINC-FINGER EXPDTA X-RAY DIFFRACTION AUTHOR M.GUO,X.-L.YANG,P.SCHIMMEL REVDAT 6 21-FEB-24 3HXY 1 REMARK REVDAT 5 13-OCT-21 3HXY 1 REMARK SEQADV LINK REVDAT 4 01-NOV-17 3HXY 1 REMARK REVDAT 3 15-FEB-12 3HXY 1 HET HETATM HETNAM HETSYN REVDAT 3 2 1 VERSN REVDAT 2 12-JAN-11 3HXY 1 JRNL REVDAT 1 15-DEC-09 3HXY 0 JRNL AUTH M.GUO,Y.E.CHONG,R.SHAPIRO,K.BEEBE,X.L.YANG,P.SCHIMMEL JRNL TITL PARADOX OF MISTRANSLATION OF SERINE FOR ALANINE CAUSED BY JRNL TITL 2 ALARS RECOGNITION DILEMMA. JRNL REF NATURE V. 462 808 2009 JRNL REFN ISSN 0028-0836 JRNL PMID 20010690 JRNL DOI 10.1038/NATURE08612 REMARK 2 REMARK 2 RESOLUTION. 2.27 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 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) : 2.27 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 41.56 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 99.9 REMARK 3 NUMBER OF REFLECTIONS : 26016 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 CROSS-VALIDATION METHOD : THROUGHOUT REMARK 3 FREE R VALUE TEST SET SELECTION : RANDOM REMARK 3 R VALUE (WORKING + TEST SET) : 0.183 REMARK 3 R VALUE (WORKING SET) : 0.181 REMARK 3 FREE R VALUE : 0.227 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.000 REMARK 3 FREE R VALUE TEST SET COUNT : 1374 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) : 2.27 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.33 REMARK 3 REFLECTION IN BIN (WORKING SET) : 1877 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 99.60 REMARK 3 BIN R VALUE (WORKING SET) : 0.1930 REMARK 3 BIN FREE R VALUE SET COUNT : 105 REMARK 3 BIN FREE R VALUE : 0.2840 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 3515 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 84 REMARK 3 SOLVENT ATOMS : 395 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 22.08 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -0.68000 REMARK 3 B22 (A**2) : 1.22000 REMARK 3 B33 (A**2) : -0.54000 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): 0.265 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.206 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.132 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 5.205 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.943 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.909 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 3691 ; 0.007 ; 0.022 REMARK 3 BOND LENGTHS OTHERS (A): NULL ; NULL ; NULL REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 5000 ; 1.002 ; 1.969 REMARK 3 BOND ANGLES OTHERS (DEGREES): NULL ; NULL ; NULL REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 444 ; 5.710 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 190 ;30.824 ;23.526 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 608 ;12.964 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 33 ;13.820 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 525 ; 0.364 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 2845 ; 0.003 ; 0.020 REMARK 3 GENERAL PLANES OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): 1904 ; 0.191 ; 0.300 REMARK 3 NON-BONDED CONTACTS OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION REFINED ATOMS (A): 2528 ; 0.321 ; 0.500 REMARK 3 NON-BONDED TORSION OTHERS (A): NULL ; NULL ; NULL REMARK 3 H-BOND (X...Y) REFINED ATOMS (A): 573 ; 0.177 ; 0.500 REMARK 3 H-BOND (X...Y) OTHERS (A): NULL ; NULL ; NULL REMARK 3 POTENTIAL METAL-ION REFINED ATOMS (A): 3 ; 0.136 ; 0.500 REMARK 3 POTENTIAL METAL-ION OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY VDW REFINED ATOMS (A): 56 ; 0.148 ; 0.300 REMARK 3 SYMMETRY VDW OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY H-BOND REFINED ATOMS (A): 31 ; 0.163 ; 0.500 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 ; 2.561 ; 2.000 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 3519 ; 3.669 ; 3.000 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 1635 ; 2.814 ; 2.000 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 1479 ; 4.008 ; 3.000 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: REMARK 3 HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS REMARK 3 LIGANDS 5AL, MDN, ACP OCCUPY THE SAME SITE REMARK 4 REMARK 4 3HXY COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 25-JUN-09. REMARK 100 THE DEPOSITION ID IS D_1000053719. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 24-JUL-08 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 8.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : SSRL REMARK 200 BEAMLINE : BL11-1 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : NULL REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : MARMOSAIC 325 MM CCD REMARK 200 INTENSITY-INTEGRATION SOFTWARE : DENZO REMARK 200 DATA SCALING SOFTWARE : SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 27449 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.270 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 : 10.10 REMARK 200 R MERGE (I) : 0.03700 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 65.3680 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.27 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.35 REMARK 200 COMPLETENESS FOR SHELL (%) : 99.9 REMARK 200 DATA REDUNDANCY IN SHELL : 10.00 REMARK 200 R MERGE FOR SHELL (I) : 0.08500 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: MOLREP REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 57.20 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.87 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 20% PEG 3350, 0.1 M TRIS-HCL, 0.2 M REMARK 280 POTASSIUM NITRATE, PH 8.5, VAPOR DIFFUSION, SITTING DROP, REMARK 280 TEMPERATURE 277K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 21 21 21 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X+1/2,-Y,Z+1/2 REMARK 290 3555 -X,Y+1/2,-Z+1/2 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 22.17750 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 59.49250 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 54.37250 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 59.49250 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 22.17750 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 54.37250 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 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: MONOMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: MONOMERIC REMARK 350 SOFTWARE USED: PISA 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 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 O8 MDN A 443 O HOH A 838 1.99 REMARK 500 O HOH A 493 O HOH A 838 2.10 REMARK 500 O HOH A 838 O HOH A 839 2.12 REMARK 500 O GLY A 72 O HOH A 759 2.15 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 THR A 35 -130.74 56.45 REMARK 500 ARG A 69 78.08 -119.74 REMARK 500 LYS A 73 -119.22 61.23 REMARK 500 ASP A 100 -123.53 -114.45 REMARK 500 PHE A 102 -138.77 -112.13 REMARK 500 TRP A 119 -128.95 -106.54 REMARK 500 ASN A 304 -130.32 57.18 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 GLY A 72 LYS A 73 67.54 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 A 445 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 GLU A 183 OE2 REMARK 620 2 GLU A 209 OE1 87.5 REMARK 620 3 5AL A 442 O2A 124.6 74.6 REMARK 620 4 MDN A 443 O3 112.4 93.1 120.4 REMARK 620 5 ACP A 444 O2B 155.7 79.2 71.3 49.0 REMARK 620 6 ACP A 444 O2A 117.4 76.4 8.0 128.3 79.3 REMARK 620 7 HOH A 804 O 116.5 151.1 101.1 63.9 72.6 103.5 REMARK 620 N 1 2 3 4 5 6 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MG A 447 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 GLU A 183 OE1 REMARK 620 2 GLU A 183 OE2 46.4 REMARK 620 3 GLU A 209 OE2 71.1 91.8 REMARK 620 4 MDN A 443 O3 152.3 133.4 81.5 REMARK 620 5 HOH A 563 O 89.7 135.5 76.8 87.9 REMARK 620 N 1 2 3 4 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MG A 448 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 GLU A 209 OE2 REMARK 620 2 ACP A 444 O3G 103.8 REMARK 620 3 ACP A 444 O2B 75.6 81.4 REMARK 620 4 HOH A 563 O 90.6 125.6 152.4 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MG A 446 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ACP A 444 O2G REMARK 620 2 ACP A 444 O1B 88.2 REMARK 620 3 HOH A 491 O 121.1 121.8 REMARK 620 4 HOH A 595 O 97.4 75.7 136.2 REMARK 620 5 HOH A 778 O 87.0 149.6 85.9 75.2 REMARK 620 6 HOH A 823 O 163.6 86.7 74.6 66.2 89.5 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 5AL A 442 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MDN A 443 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ACP A 444 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MG A 445 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MG A 446 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MG A 447 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC7 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MG A 448 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC8 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE HED A 449 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC9 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE BME A 450 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 3HXU RELATED DB: PDB REMARK 900 SAME PROTEIN WITH G237A MUTATION, COMPLEXED WITH SERSA REMARK 900 RELATED ID: 3HXV RELATED DB: PDB REMARK 900 SAME PROTEIN IN COMPLEX WITH GLYSA REMARK 900 RELATED ID: 3HXW RELATED DB: PDB REMARK 900 SAME PROTEIN IN COMPLEX WITH SERSA REMARK 900 RELATED ID: 3HXX RELATED DB: PDB REMARK 900 SAME PROTEIN IN COMPLEX WITH AMPPCP REMARK 900 RELATED ID: 3HXZ RELATED DB: PDB REMARK 900 SAME PROTEIN WITH G237A MUTATION, IN COMPLEX WITH ALASA REMARK 900 RELATED ID: 3HY0 RELATED DB: PDB REMARK 900 SAME PROTEIN WITH ALARS G237A MUTATION, IN COMPLEX WITH GLYSA REMARK 900 RELATED ID: 3HY1 RELATED DB: PDB REMARK 900 SAME PROTEIN WITH G237A MUTATION, IN COMPLEX WITH SERSA DBREF 3HXY A 1 441 UNP P00957 SYA_ECOLI 2 442 SEQADV 3HXY LEU A 104 UNP P00957 HIS 105 ENGINEERED MUTATION SEQADV 3HXY LEU A 108 UNP P00957 GLN 109 ENGINEERED MUTATION SEQADV 3HXY LEU A 112 UNP P00957 GLU 113 ENGINEERED MUTATION SEQRES 1 A 441 SER LYS SER THR ALA GLU ILE ARG GLN ALA PHE LEU ASP SEQRES 2 A 441 PHE PHE HIS SER LYS GLY HIS GLN VAL VAL ALA SER SER SEQRES 3 A 441 SER LEU VAL PRO HIS ASN ASP PRO THR LEU LEU PHE THR SEQRES 4 A 441 ASN ALA GLY MET ASN GLN PHE LYS ASP VAL PHE LEU GLY SEQRES 5 A 441 LEU ASP LYS ARG ASN TYR SER ARG ALA THR THR SER GLN SEQRES 6 A 441 ARG CYS VAL ARG ALA GLY GLY LYS HIS ASN ASP LEU GLU SEQRES 7 A 441 ASN VAL GLY TYR THR ALA ARG HIS HIS THR PHE PHE GLU SEQRES 8 A 441 MET LEU GLY ASN PHE SER PHE GLY ASP TYR PHE LYS LEU SEQRES 9 A 441 ASP ALA ILE LEU PHE ALA TRP LEU LEU LEU THR SER GLU SEQRES 10 A 441 LYS TRP PHE ALA LEU PRO LYS GLU ARG LEU TRP VAL THR SEQRES 11 A 441 VAL TYR GLU SER ASP ASP GLU ALA TYR GLU ILE TRP GLU SEQRES 12 A 441 LYS GLU VAL GLY ILE PRO ARG GLU ARG ILE ILE ARG ILE SEQRES 13 A 441 GLY ASP ASN LYS GLY ALA PRO TYR ALA SER ASP ASN PHE SEQRES 14 A 441 TRP GLN MET GLY ASP THR GLY PRO CYS GLY PRO CYS THR SEQRES 15 A 441 GLU ILE PHE TYR ASP HIS GLY ASP HIS ILE TRP GLY GLY SEQRES 16 A 441 PRO PRO GLY SER PRO GLU GLU ASP GLY ASP ARG TYR ILE SEQRES 17 A 441 GLU ILE TRP ASN ILE VAL PHE MET GLN PHE ASN ARG GLN SEQRES 18 A 441 ALA ASP GLY THR MET GLU PRO LEU PRO LYS PRO SER VAL SEQRES 19 A 441 ASP THR GLY MET GLY LEU GLU ARG ILE ALA ALA VAL LEU SEQRES 20 A 441 GLN HIS VAL ASN SER ASN TYR ASP ILE ASP LEU PHE ARG SEQRES 21 A 441 THR LEU ILE GLN ALA VAL ALA LYS VAL THR GLY ALA THR SEQRES 22 A 441 ASP LEU SER ASN LYS SER LEU ARG VAL ILE ALA ASP HIS SEQRES 23 A 441 ILE ARG SER CYS ALA PHE LEU ILE ALA ASP GLY VAL MET SEQRES 24 A 441 PRO SER ASN GLU ASN ARG GLY TYR VAL LEU ARG ARG ILE SEQRES 25 A 441 ILE ARG ARG ALA VAL ARG HIS GLY ASN MET LEU GLY ALA SEQRES 26 A 441 LYS GLU THR PHE PHE TYR LYS LEU VAL GLY PRO LEU ILE SEQRES 27 A 441 ASP VAL MET GLY SER ALA GLY GLU ASP LEU LYS ARG GLN SEQRES 28 A 441 GLN ALA GLN VAL GLU GLN VAL LEU LYS THR GLU GLU GLU SEQRES 29 A 441 GLN PHE ALA ARG THR LEU GLU ARG GLY LEU ALA LEU LEU SEQRES 30 A 441 ASP GLU GLU LEU ALA LYS LEU SER GLY ASP THR LEU ASP SEQRES 31 A 441 GLY GLU THR ALA PHE ARG LEU TYR ASP THR TYR GLY PHE SEQRES 32 A 441 PRO VAL ASP LEU THR ALA ASP VAL CYS ARG GLU ARG ASN SEQRES 33 A 441 ILE LYS VAL ASP GLU ALA GLY PHE GLU ALA ALA MET GLU SEQRES 34 A 441 GLU GLN ARG ARG ARG ALA ARG GLU ALA SER GLY PHE HET 5AL A 442 28 HET MDN A 443 9 HET ACP A 444 31 HET MG A 445 1 HET MG A 446 1 HET MG A 447 1 HET MG A 448 1 HET HED A 449 8 HET BME A 450 4 HETNAM 5AL 5'-O-[(R)-{[(2S)-2-AMINOPROPANOYL]OXY}(HYDROXY) HETNAM 2 5AL PHOSPHORYL]ADENOSINE HETNAM MDN METHYLENEDIPHOSPHONIC ACID HETNAM ACP PHOSPHOMETHYLPHOSPHONIC ACID ADENYLATE ESTER HETNAM MG MAGNESIUM ION HETNAM HED 2-HYDROXYETHYL DISULFIDE HETNAM BME BETA-MERCAPTOETHANOL HETSYN 5AL ALANYL ADENYLATE HETSYN ACP ADENOSINE-5'-[BETA, GAMMA-METHYLENE]TRIPHOSPHATE FORMUL 2 5AL C13 H19 N6 O8 P FORMUL 3 MDN C H6 O6 P2 FORMUL 4 ACP C11 H18 N5 O12 P3 FORMUL 5 MG 4(MG 2+) FORMUL 9 HED C4 H10 O2 S2 FORMUL 10 BME C2 H6 O S FORMUL 11 HOH *395(H2 O) HELIX 1 1 SER A 3 SER A 17 1 15 HELIX 2 2 MET A 43 GLN A 45 5 3 HELIX 3 3 PHE A 46 LEU A 51 1 6 HELIX 4 4 PHE A 102 SER A 116 1 15 HELIX 5 5 PRO A 123 GLU A 125 5 3 HELIX 6 6 ASP A 135 GLU A 145 1 11 HELIX 7 7 PRO A 149 GLU A 151 5 3 HELIX 8 8 LEU A 240 GLN A 248 1 9 HELIX 9 9 SER A 252 ASP A 255 5 4 HELIX 10 10 ILE A 256 GLY A 271 1 16 HELIX 11 11 ASN A 277 ASP A 296 1 20 HELIX 12 12 GLU A 303 GLY A 324 1 22 HELIX 13 13 PHE A 329 LYS A 332 5 4 HELIX 14 14 LEU A 333 GLY A 342 1 10 HELIX 15 15 GLY A 345 ARG A 350 1 6 HELIX 16 16 GLN A 351 ARG A 368 1 18 HELIX 17 17 THR A 369 ALA A 382 1 14 HELIX 18 18 ASP A 390 THR A 400 1 11 HELIX 19 19 PRO A 404 GLU A 414 1 11 HELIX 20 20 ASP A 420 GLY A 440 1 21 SHEET 1 A 8 GLN A 21 VAL A 22 0 SHEET 2 A 8 ARG A 60 VAL A 68 1 O ARG A 60 N GLN A 21 SHEET 3 A 8 PHE A 89 SER A 97 -1 O PHE A 96 N ALA A 61 SHEET 4 A 8 MET A 226 GLY A 239 -1 O MET A 238 N LEU A 93 SHEET 5 A 8 TYR A 207 ARG A 220 -1 N ASN A 219 O GLU A 227 SHEET 6 A 8 GLY A 176 ASP A 187 -1 N CYS A 178 O PHE A 218 SHEET 7 A 8 LEU A 127 TYR A 132 -1 N TRP A 128 O PHE A 185 SHEET 8 A 8 ILE A 153 ILE A 156 1 O ILE A 154 N VAL A 129 SHEET 1 B 7 GLN A 21 VAL A 22 0 SHEET 2 B 7 ARG A 60 VAL A 68 1 O ARG A 60 N GLN A 21 SHEET 3 B 7 PHE A 89 SER A 97 -1 O PHE A 96 N ALA A 61 SHEET 4 B 7 MET A 226 GLY A 239 -1 O MET A 238 N LEU A 93 SHEET 5 B 7 TYR A 207 ARG A 220 -1 N ASN A 219 O GLU A 227 SHEET 6 B 7 GLY A 176 ASP A 187 -1 N CYS A 178 O PHE A 218 SHEET 7 B 7 PHE A 169 GLN A 171 -1 N TRP A 170 O GLY A 179 SHEET 1 C 2 ALA A 70 GLY A 71 0 SHEET 2 C 2 HIS A 74 ASN A 75 -1 O HIS A 74 N GLY A 71 SHEET 1 D 2 THR A 388 LEU A 389 0 SHEET 2 D 2 LYS A 418 VAL A 419 1 O LYS A 418 N LEU A 389 LINK OE2 GLU A 183 MG MG A 445 1555 1555 2.40 LINK OE1 GLU A 183 MG A MG A 447 1555 1555 2.58 LINK OE2 GLU A 183 MG A MG A 447 1555 1555 2.94 LINK OE1 GLU A 209 MG MG A 445 1555 1555 2.56 LINK OE2 GLU A 209 MG A MG A 447 1555 1555 2.62 LINK OE2 GLU A 209 MG B MG A 448 1555 1555 2.28 LINK O2AA5AL A 442 MG MG A 445 1555 1555 2.59 LINK O3 AMDN A 443 MG MG A 445 1555 1555 3.00 LINK O3 AMDN A 443 MG A MG A 447 1555 1555 1.94 LINK O2BBACP A 444 MG MG A 445 1555 1555 1.77 LINK O2ABACP A 444 MG MG A 445 1555 1555 2.46 LINK O2GBACP A 444 MG B MG A 446 1555 1555 1.88 LINK O1BBACP A 444 MG B MG A 446 1555 1555 2.14 LINK O3GBACP A 444 MG B MG A 448 1555 1555 1.89 LINK O2BBACP A 444 MG B MG A 448 1555 1555 2.91 LINK MG MG A 445 O HOH A 804 1555 1555 2.50 LINK MG B MG A 446 O HOH A 491 1555 1555 2.47 LINK MG B MG A 446 O HOH A 595 1555 1555 2.72 LINK MG B MG A 446 O HOH A 778 1555 1555 1.91 LINK MG B MG A 446 O HOH A 823 1555 1555 1.96 LINK MG A MG A 447 O HOH A 563 1555 1555 2.54 LINK MG B MG A 448 O HOH A 563 1555 1555 2.23 CISPEP 1 PRO A 34 THR A 35 0 -21.14 SITE 1 AC1 22 ALA A 41 ARG A 69 ASP A 76 ARG A 85 SITE 2 AC1 22 HIS A 86 HIS A 87 PHE A 90 MET A 92 SITE 3 AC1 22 TRP A 170 GLU A 209 ILE A 210 ASN A 212 SITE 4 AC1 22 ASP A 235 THR A 236 GLY A 237 GLY A 239 SITE 5 AC1 22 ARG A 242 MG A 445 HOH A 457 HOH A 459 SITE 6 AC1 22 HOH A 581 HOH A 595 SITE 1 AC2 17 ARG A 85 HIS A 86 GLU A 209 ARG A 242 SITE 2 AC2 17 MG A 445 MG A 446 MG A 447 HOH A 474 SITE 3 AC2 17 HOH A 491 HOH A 494 HOH A 563 HOH A 778 SITE 4 AC2 17 HOH A 804 HOH A 824 HOH A 838 HOH A 839 SITE 5 AC2 17 HOH A 841 SITE 1 AC3 26 ARG A 69 ASP A 76 ARG A 85 HIS A 86 SITE 2 AC3 26 HIS A 87 PHE A 90 MET A 92 TRP A 170 SITE 3 AC3 26 GLU A 209 ILE A 210 ASN A 212 GLY A 237 SITE 4 AC3 26 GLY A 239 ARG A 242 MG A 445 MG A 446 SITE 5 AC3 26 MG A 447 MG A 448 HOH A 457 HOH A 474 SITE 6 AC3 26 HOH A 581 HOH A 595 HOH A 778 HOH A 804 SITE 7 AC3 26 HOH A 823 HOH A 824 SITE 1 AC4 10 GLU A 183 GLU A 209 ASN A 212 5AL A 442 SITE 2 AC4 10 MDN A 443 ACP A 444 MG A 447 MG A 448 SITE 3 AC4 10 HOH A 570 HOH A 804 SITE 1 AC5 6 MDN A 443 ACP A 444 HOH A 491 HOH A 595 SITE 2 AC5 6 HOH A 778 HOH A 823 SITE 1 AC6 7 ASP A 167 GLU A 183 GLU A 209 MDN A 443 SITE 2 AC6 7 ACP A 444 MG A 445 HOH A 563 SITE 1 AC7 4 GLU A 209 ACP A 444 MG A 445 HOH A 563 SITE 1 AC8 5 LYS A 2 LYS A 118 TRP A 119 PHE A 120 SITE 2 AC8 5 HOH A 538 SITE 1 AC9 1 TRP A 193 CRYST1 44.355 108.745 118.985 90.00 90.00 90.00 P 21 21 21 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 0.022545 0.000000 0.000000 0.00000 SCALE2 0.000000 0.009196 0.000000 0.00000 SCALE3 0.000000 0.000000 0.008404 0.00000