HEADER LIGASE 22-JUN-09 3HY1 TITLE CRYSTAL STRUCTURE OF CATALYTIC FRAGMENT OF E. COLI ALARS G237A IN TITLE 2 COMPLEX WITH SERSA COMPND MOL_ID: 1; COMPND 2 MOLECULE: ALANYL-TRNA SYNTHETASE; COMPND 3 CHAIN: A, B; 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 5 21-FEB-24 3HY1 1 REMARK REVDAT 4 13-OCT-21 3HY1 1 REMARK SEQADV REVDAT 3 01-NOV-17 3HY1 1 REMARK REVDAT 2 12-JAN-11 3HY1 1 JRNL REVDAT 1 15-DEC-09 3HY1 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. 2.79 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) : 2.79 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 46.47 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.8 REMARK 3 NUMBER OF REFLECTIONS : 34133 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) : 0.231 REMARK 3 R VALUE (WORKING SET) : 0.229 REMARK 3 FREE R VALUE : 0.266 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.100 REMARK 3 FREE R VALUE TEST SET COUNT : 1727 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) : 2.79 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.87 REMARK 3 REFLECTION IN BIN (WORKING SET) : 2335 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 97.99 REMARK 3 BIN R VALUE (WORKING SET) : 0.3010 REMARK 3 BIN FREE R VALUE SET COUNT : 103 REMARK 3 BIN FREE R VALUE : 0.3460 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 6860 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 55 REMARK 3 SOLVENT ATOMS : 73 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 52.65 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 1.21000 REMARK 3 B22 (A**2) : -0.58000 REMARK 3 B33 (A**2) : -0.63000 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): 0.815 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.351 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.265 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 13.270 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.921 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.904 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 7063 ; 0.007 ; 0.022 REMARK 3 BOND LENGTHS OTHERS (A): NULL ; NULL ; NULL REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 9547 ; 0.956 ; 1.952 REMARK 3 BOND ANGLES OTHERS (DEGREES): NULL ; NULL ; NULL REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 857 ; 7.871 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 364 ;32.556 ;23.516 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 1184 ;15.999 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 63 ;18.153 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 1020 ; 0.066 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 5456 ; 0.004 ; 0.020 REMARK 3 GENERAL PLANES OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): 3375 ; 0.227 ; 0.300 REMARK 3 NON-BONDED CONTACTS OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION REFINED ATOMS (A): 4864 ; 0.329 ; 0.500 REMARK 3 NON-BONDED TORSION OTHERS (A): NULL ; NULL ; NULL REMARK 3 H-BOND (X...Y) REFINED ATOMS (A): 449 ; 0.233 ; 0.500 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): 64 ; 0.219 ; 0.300 REMARK 3 SYMMETRY VDW OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY H-BOND REFINED ATOMS (A): 15 ; 0.210 ; 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): 4342 ; 0.767 ; 2.000 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 6834 ; 1.283 ; 3.000 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 3005 ; 0.571 ; 2.000 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 2713 ; 0.841 ; 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: HYDROGENS HAVE BEEN ADDED IN THE RIDING REMARK 3 POSITIONS REMARK 4 REMARK 4 3HY1 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_1000053722. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 12-MAY-09 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 6.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : SSRL REMARK 200 BEAMLINE : BL7-1 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.97971 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 315R REMARK 200 INTENSITY-INTEGRATION SOFTWARE : DENZO REMARK 200 DATA SCALING SOFTWARE : SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 34198 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.790 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 (%) : 99.9 REMARK 200 DATA REDUNDANCY : 14.10 REMARK 200 R MERGE (I) : 0.09700 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 29.5490 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.79 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.90 REMARK 200 COMPLETENESS FOR SHELL (%) : 99.7 REMARK 200 DATA REDUNDANCY IN SHELL : 12.60 REMARK 200 R MERGE FOR SHELL (I) : 0.46700 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: NULL REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 63.47 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 3.37 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 25% PEGMME550, 0.1 M MES, 0.2 M SODIUM REMARK 280 SULFATE, PH 6.5, VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 296K 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 38.15400 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 75.27500 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 58.54600 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 75.27500 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 38.15400 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 58.54600 REMARK 290 SMTRY3 4 0.000000 0.000000 -1.000000 0.00000 REMARK 290 REMARK 290 REMARK: NULL REMARK 300 REMARK 300 BIOMOLECULE: 1, 2 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 350 REMARK 350 BIOMOLECULE: 2 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: B 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 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 PHE A 441 REMARK 465 GLY B 189 REMARK 465 ASP B 190 REMARK 465 HIS B 191 REMARK 465 ILE B 192 REMARK 465 TRP B 193 REMARK 465 GLY B 194 REMARK 465 GLY B 195 REMARK 465 PRO B 196 REMARK 465 PRO B 197 REMARK 465 GLY B 198 REMARK 465 SER B 199 REMARK 465 PRO B 200 REMARK 465 GLU B 201 REMARK 465 GLU B 202 REMARK 465 ASP B 203 REMARK 465 GLY B 204 REMARK 465 ASP B 205 REMARK 465 ALA B 438 REMARK 465 SER B 439 REMARK 465 GLY B 440 REMARK 465 PHE B 441 REMARK 470 REMARK 470 MISSING ATOM REMARK 470 THE FOLLOWING RESIDUES HAVE MISSING ATOMS (M=MODEL NUMBER; REMARK 470 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; REMARK 470 I=INSERTION CODE): REMARK 470 M RES CSSEQI ATOMS REMARK 470 GLU B 430 CG CD OE1 OE2 REMARK 470 ARG B 436 CG CD NE CZ NH1 NH2 REMARK 470 GLU B 437 CG CD OE1 OE2 REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CLOSE CONTACTS IN SAME ASYMMETRIC UNIT REMARK 500 REMARK 500 THE FOLLOWING ATOMS ARE IN CLOSE CONTACT. REMARK 500 REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI DISTANCE REMARK 500 OD1 ASP A 235 OG SSA A 442 1.86 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 PRO A 34 C - N - CA ANGL. DEV. = 9.9 DEGREES REMARK 500 TYR A 164 C - N - CA ANGL. DEV. = -15.7 DEGREES REMARK 500 GLY B 72 N - CA - C ANGL. DEV. = -18.5 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 100 -125.44 -102.04 REMARK 500 PHE A 102 -136.25 -114.20 REMARK 500 TRP A 119 -123.14 -89.83 REMARK 500 ASP A 158 69.79 -67.86 REMARK 500 TYR A 164 93.71 -55.90 REMARK 500 ALA A 222 -88.73 159.41 REMARK 500 ASN A 304 -127.14 56.35 REMARK 500 ASP B 100 -108.02 -102.73 REMARK 500 PHE B 102 -150.93 -146.65 REMARK 500 TRP B 119 -141.18 -111.17 REMARK 500 ASN B 304 -128.39 57.88 REMARK 500 ASN B 416 38.97 73.33 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 PHE A 120 ALA A 121 -132.36 REMARK 500 PRO A 163 TYR A 164 -97.05 REMARK 500 GLU B 430 GLN B 431 -148.84 REMARK 500 GLN B 431 ARG B 432 -136.46 REMARK 500 ARG B 434 ALA B 435 133.56 REMARK 500 REMARK 500 REMARK: NULL REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SSA A 442 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE HED A 443 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SO4 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 MES B 442 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: 3HXY RELATED DB: PDB REMARK 900 SAME PROTEIN IN COMPLEX WITH AMPPCP, ALA-AMP AND PCP 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 DBREF 3HY1 A 1 441 UNP P00957 SYA_ECOLI 2 442 DBREF 3HY1 B 1 441 UNP P00957 SYA_ECOLI 2 442 SEQADV 3HY1 LEU A 104 UNP P00957 HIS 105 ENGINEERED MUTATION SEQADV 3HY1 LEU A 108 UNP P00957 GLN 109 ENGINEERED MUTATION SEQADV 3HY1 LEU A 112 UNP P00957 GLU 113 ENGINEERED MUTATION SEQADV 3HY1 ALA A 237 UNP P00957 GLY 238 ENGINEERED MUTATION SEQADV 3HY1 LEU B 104 UNP P00957 HIS 105 ENGINEERED MUTATION SEQADV 3HY1 LEU B 108 UNP P00957 GLN 109 ENGINEERED MUTATION SEQADV 3HY1 LEU B 112 UNP P00957 GLU 113 ENGINEERED MUTATION SEQADV 3HY1 ALA B 237 UNP P00957 GLY 238 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 ALA 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 SEQRES 1 B 441 SER LYS SER THR ALA GLU ILE ARG GLN ALA PHE LEU ASP SEQRES 2 B 441 PHE PHE HIS SER LYS GLY HIS GLN VAL VAL ALA SER SER SEQRES 3 B 441 SER LEU VAL PRO HIS ASN ASP PRO THR LEU LEU PHE THR SEQRES 4 B 441 ASN ALA GLY MET ASN GLN PHE LYS ASP VAL PHE LEU GLY SEQRES 5 B 441 LEU ASP LYS ARG ASN TYR SER ARG ALA THR THR SER GLN SEQRES 6 B 441 ARG CYS VAL ARG ALA GLY GLY LYS HIS ASN ASP LEU GLU SEQRES 7 B 441 ASN VAL GLY TYR THR ALA ARG HIS HIS THR PHE PHE GLU SEQRES 8 B 441 MET LEU GLY ASN PHE SER PHE GLY ASP TYR PHE LYS LEU SEQRES 9 B 441 ASP ALA ILE LEU PHE ALA TRP LEU LEU LEU THR SER GLU SEQRES 10 B 441 LYS TRP PHE ALA LEU PRO LYS GLU ARG LEU TRP VAL THR SEQRES 11 B 441 VAL TYR GLU SER ASP ASP GLU ALA TYR GLU ILE TRP GLU SEQRES 12 B 441 LYS GLU VAL GLY ILE PRO ARG GLU ARG ILE ILE ARG ILE SEQRES 13 B 441 GLY ASP ASN LYS GLY ALA PRO TYR ALA SER ASP ASN PHE SEQRES 14 B 441 TRP GLN MET GLY ASP THR GLY PRO CYS GLY PRO CYS THR SEQRES 15 B 441 GLU ILE PHE TYR ASP HIS GLY ASP HIS ILE TRP GLY GLY SEQRES 16 B 441 PRO PRO GLY SER PRO GLU GLU ASP GLY ASP ARG TYR ILE SEQRES 17 B 441 GLU ILE TRP ASN ILE VAL PHE MET GLN PHE ASN ARG GLN SEQRES 18 B 441 ALA ASP GLY THR MET GLU PRO LEU PRO LYS PRO SER VAL SEQRES 19 B 441 ASP THR ALA MET GLY LEU GLU ARG ILE ALA ALA VAL LEU SEQRES 20 B 441 GLN HIS VAL ASN SER ASN TYR ASP ILE ASP LEU PHE ARG SEQRES 21 B 441 THR LEU ILE GLN ALA VAL ALA LYS VAL THR GLY ALA THR SEQRES 22 B 441 ASP LEU SER ASN LYS SER LEU ARG VAL ILE ALA ASP HIS SEQRES 23 B 441 ILE ARG SER CYS ALA PHE LEU ILE ALA ASP GLY VAL MET SEQRES 24 B 441 PRO SER ASN GLU ASN ARG GLY TYR VAL LEU ARG ARG ILE SEQRES 25 B 441 ILE ARG ARG ALA VAL ARG HIS GLY ASN MET LEU GLY ALA SEQRES 26 B 441 LYS GLU THR PHE PHE TYR LYS LEU VAL GLY PRO LEU ILE SEQRES 27 B 441 ASP VAL MET GLY SER ALA GLY GLU ASP LEU LYS ARG GLN SEQRES 28 B 441 GLN ALA GLN VAL GLU GLN VAL LEU LYS THR GLU GLU GLU SEQRES 29 B 441 GLN PHE ALA ARG THR LEU GLU ARG GLY LEU ALA LEU LEU SEQRES 30 B 441 ASP GLU GLU LEU ALA LYS LEU SER GLY ASP THR LEU ASP SEQRES 31 B 441 GLY GLU THR ALA PHE ARG LEU TYR ASP THR TYR GLY PHE SEQRES 32 B 441 PRO VAL ASP LEU THR ALA ASP VAL CYS ARG GLU ARG ASN SEQRES 33 B 441 ILE LYS VAL ASP GLU ALA GLY PHE GLU ALA ALA MET GLU SEQRES 34 B 441 GLU GLN ARG ARG ARG ALA ARG GLU ALA SER GLY PHE HET SSA A 442 29 HET HED A 443 8 HET SO4 A 444 5 HET MG A 445 1 HET MES B 442 12 HETNAM SSA 5'-O-(N-(L-SERYL)-SULFAMOYL)ADENOSINE HETNAM HED 2-HYDROXYETHYL DISULFIDE HETNAM SO4 SULFATE ION HETNAM MG MAGNESIUM ION HETNAM MES 2-(N-MORPHOLINO)-ETHANESULFONIC ACID FORMUL 3 SSA C13 H19 N7 O8 S FORMUL 4 HED C4 H10 O2 S2 FORMUL 5 SO4 O4 S 2- FORMUL 6 MG MG 2+ FORMUL 7 MES C6 H13 N O4 S FORMUL 8 HOH *73(H2 O) HELIX 1 1 SER A 3 LYS A 18 1 16 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 LEU A 77 VAL A 80 5 4 HELIX 5 5 PHE A 102 SER A 116 1 15 HELIX 6 6 ASP A 135 LYS A 144 1 10 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 VAL A 340 1 8 HELIX 15 15 MET A 341 ALA A 344 5 4 HELIX 16 16 GLY A 345 GLN A 351 1 7 HELIX 17 17 GLN A 352 LYS A 383 1 32 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 SER A 439 1 20 HELIX 21 21 SER B 3 SER B 17 1 15 HELIX 22 22 ALA B 41 GLN B 45 5 5 HELIX 23 23 PHE B 46 GLY B 52 1 7 HELIX 24 24 LEU B 77 VAL B 80 5 4 HELIX 25 25 PHE B 102 SER B 116 1 15 HELIX 26 26 PRO B 123 GLU B 125 5 3 HELIX 27 27 ASP B 135 GLU B 145 1 11 HELIX 28 28 PRO B 149 GLU B 151 5 3 HELIX 29 29 LEU B 240 GLN B 248 1 9 HELIX 30 30 SER B 252 ASP B 255 5 4 HELIX 31 31 ILE B 256 GLY B 271 1 16 HELIX 32 32 ASN B 277 ASP B 296 1 20 HELIX 33 33 GLU B 303 GLY B 324 1 22 HELIX 34 34 PHE B 329 LYS B 332 5 4 HELIX 35 35 LEU B 333 GLY B 342 1 10 HELIX 36 36 GLY B 345 GLN B 351 1 7 HELIX 37 37 GLN B 351 GLN B 365 1 15 HELIX 38 38 PHE B 366 LYS B 383 1 18 HELIX 39 39 ASP B 390 THR B 400 1 11 HELIX 40 40 PRO B 404 ARG B 415 1 12 HELIX 41 41 ASP B 420 ARG B 434 1 15 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 VAL A 214 O ASP A 235 SHEET 6 A 8 GLY A 176 ASP A 187 -1 N ILE A 184 O ILE A 210 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 156 N VAL A 131 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 VAL A 214 O ASP A 235 SHEET 6 B 7 GLY A 176 ASP A 187 -1 N ILE A 184 O ILE A 210 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 SHEET 1 E 8 GLN B 21 VAL B 22 0 SHEET 2 E 8 ARG B 60 VAL B 68 1 O ARG B 60 N GLN B 21 SHEET 3 E 8 PHE B 89 SER B 97 -1 O PHE B 90 N CYS B 67 SHEET 4 E 8 MET B 226 GLY B 239 -1 O MET B 238 N LEU B 93 SHEET 5 E 8 ILE B 208 ARG B 220 -1 N GLN B 217 O LEU B 229 SHEET 6 E 8 GLY B 176 TYR B 186 -1 N ILE B 184 O ILE B 210 SHEET 7 E 8 LEU B 127 TYR B 132 -1 N TRP B 128 O PHE B 185 SHEET 8 E 8 ILE B 153 ILE B 156 1 O ILE B 154 N VAL B 129 SHEET 1 F 7 GLN B 21 VAL B 22 0 SHEET 2 F 7 ARG B 60 VAL B 68 1 O ARG B 60 N GLN B 21 SHEET 3 F 7 PHE B 89 SER B 97 -1 O PHE B 90 N CYS B 67 SHEET 4 F 7 MET B 226 GLY B 239 -1 O MET B 238 N LEU B 93 SHEET 5 F 7 ILE B 208 ARG B 220 -1 N GLN B 217 O LEU B 229 SHEET 6 F 7 GLY B 176 TYR B 186 -1 N ILE B 184 O ILE B 210 SHEET 7 F 7 PHE B 169 GLN B 171 -1 N TRP B 170 O GLY B 179 SHEET 1 G 2 ALA B 70 GLY B 71 0 SHEET 2 G 2 HIS B 74 ASN B 75 -1 O HIS B 74 N GLY B 71 SHEET 1 H 2 THR B 388 LEU B 389 0 SHEET 2 H 2 LYS B 418 VAL B 419 1 O LYS B 418 N LEU B 389 LINK OE1 GLU A 209 MG MG A 445 1555 1555 3.00 CISPEP 1 GLY B 72 LYS B 73 0 16.15 SITE 1 AC1 17 ARG A 69 ASP A 76 ARG A 85 HIS A 86 SITE 2 AC1 17 HIS A 87 PHE A 90 MET A 92 TRP A 170 SITE 3 AC1 17 GLU A 209 ILE A 210 ASN A 212 ASP A 235 SITE 4 AC1 17 ALA A 237 GLY A 239 ARG A 242 MG A 445 SITE 5 AC1 17 HOH A 470 SITE 1 AC2 3 TYR A 398 ASP A 399 HOH A 453 SITE 1 AC3 5 ARG A 85 HIS A 86 GLU A 209 ARG A 242 SITE 2 AC3 5 MG A 445 SITE 1 AC4 3 GLU A 209 SSA A 442 SO4 A 444 SITE 1 AC5 6 VAL B 29 HIS B 31 ARG B 60 ASP B 105 SITE 2 AC5 6 ASP B 296 GLY B 297 CRYST1 76.308 117.092 150.550 90.00 90.00 90.00 P 21 21 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 0.013105 0.000000 0.000000 0.00000 SCALE2 0.000000 0.008540 0.000000 0.00000 SCALE3 0.000000 0.000000 0.006642 0.00000