PDB Short entry for 1YFT HEADER LIGASE 03-JAN-05 1YFT TITLE THE CRYSTAL STRUCTURE OF THE CATALYTIC FRAGMENT OF ALANYL-TRNA TITLE 2 SYNTHETASE IN COMPLEX WTIH GLYCINE COMPND MOL_ID: 1; COMPND 2 MOLECULE: ALANYL-TRNA SYNTHETASE; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: ALANINE-TRNA LIGASE, ALARS; COMPND 5 EC: 6.1.1.7; COMPND 6 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: AQUIFEX AEOLICUS; SOURCE 3 ORGANISM_TAXID: 63363; SOURCE 4 GENE: ALAS; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 6 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 7 EXPRESSION_SYSTEM_STRAIN: B834(DE3); SOURCE 8 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 9 EXPRESSION_SYSTEM_PLASMID: PET20B+ KEYWDS ALPHA-BETA FOLD, AMINO ACID BINDING, HELIX-LOOP HELIX MOTIF, LIGASE EXPDTA X-RAY DIFFRACTION AUTHOR M.A.SWAIRJO,P.R.SCHIMMEL REVDAT 4 23-AUG-23 1YFT 1 REMARK SEQADV REVDAT 3 24-FEB-09 1YFT 1 VERSN REVDAT 2 08-FEB-05 1YFT 1 JRNL REVDAT 1 25-JAN-05 1YFT 0 JRNL AUTH M.A.SWAIRJO,P.R.SCHIMMEL JRNL TITL BREAKING SIEVE FOR STERIC EXCLUSION OF A NONCOGNATE AMINO JRNL TITL 2 ACID FROM ACTIVE SITE OF A TRNA SYNTHETASE. JRNL REF PROC.NATL.ACAD.SCI.USA V. 102 988 2005 JRNL REFN ISSN 0027-8424 JRNL PMID 15657145 JRNL DOI 10.1073/PNAS.0409024102 REMARK 1 REMARK 1 REFERENCE 1 REMARK 1 AUTH M.A.SWAIRJO,F.J.OTERO,X.-L.YANG,M.A.LOVATO,R.J.SKENE, REMARK 1 AUTH 2 D.E.MCREE,L.RIBAS DE POUPLANA,P.SCHIMMEL REMARK 1 TITL ALANYL-TRNA SYNTHETASE CRYSTAL STRUCTURE AND DESIGN FOR REMARK 1 TITL 2 ACCEPTOR-STEM RECOGNITION. REMARK 1 REF MOL.CELL V. 13 829 2004 REMARK 1 REFN ISSN 1097-2765 REMARK 1 PMID 15053876 REMARK 1 DOI 10.1016/S1097-2765(04)00126-1 REMARK 2 REMARK 2 RESOLUTION. 2.23 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : CNS REMARK 3 AUTHORS : BRUNGER,ADAMS,CLORE,DELANO,GROS,GROSSE- REMARK 3 : KUNSTLEVE,JIANG,KUSZEWSKI,NILGES,PANNU, REMARK 3 : READ,RICE,SIMONSON,WARREN REMARK 3 REMARK 3 REFINEMENT TARGET : ENGH & HUBER REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.23 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 50.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 DATA CUTOFF HIGH (ABS(F)) : NULL REMARK 3 DATA CUTOFF LOW (ABS(F)) : NULL REMARK 3 COMPLETENESS (WORKING+TEST) (%) : NULL REMARK 3 NUMBER OF REFLECTIONS : 24100 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 SET) : 0.207 REMARK 3 FREE R VALUE : 0.239 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 10.000 REMARK 3 FREE R VALUE TEST SET COUNT : 2384 REMARK 3 ESTIMATED ERROR OF FREE R VALUE : NULL REMARK 3 REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN. REMARK 3 TOTAL NUMBER OF BINS USED : 8 REMARK 3 BIN RESOLUTION RANGE HIGH (A) : 2.23 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.33 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 99.30 REMARK 3 REFLECTIONS IN BIN (WORKING SET) : 2476 REMARK 3 BIN R VALUE (WORKING SET) : NULL REMARK 3 BIN FREE R VALUE : 0.2160 REMARK 3 BIN FREE R VALUE TEST SET SIZE (%) : 9.00 REMARK 3 BIN FREE R VALUE TEST SET COUNT : 286 REMARK 3 ESTIMATED ERROR OF BIN FREE R VALUE : 0.233 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 3641 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 5 REMARK 3 SOLVENT ATOMS : 193 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 21.90 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : NULL REMARK 3 B22 (A**2) : NULL REMARK 3 B33 (A**2) : NULL REMARK 3 B12 (A**2) : NULL REMARK 3 B13 (A**2) : NULL REMARK 3 B23 (A**2) : NULL REMARK 3 REMARK 3 ESTIMATED COORDINATE ERROR. REMARK 3 ESD FROM LUZZATI PLOT (A) : NULL REMARK 3 ESD FROM SIGMAA (A) : NULL REMARK 3 LOW RESOLUTION CUTOFF (A) : NULL REMARK 3 REMARK 3 CROSS-VALIDATED ESTIMATED COORDINATE ERROR. REMARK 3 ESD FROM C-V LUZZATI PLOT (A) : NULL REMARK 3 ESD FROM C-V SIGMAA (A) : NULL REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES. REMARK 3 BOND LENGTHS (A) : 0.019 REMARK 3 BOND ANGLES (DEGREES) : 1.431 REMARK 3 DIHEDRAL ANGLES (DEGREES) : NULL REMARK 3 IMPROPER ANGLES (DEGREES) : NULL REMARK 3 REMARK 3 ISOTROPIC THERMAL MODEL : ISOTROPIC REMARK 3 REMARK 3 ISOTROPIC THERMAL FACTOR RESTRAINTS. RMS SIGMA REMARK 3 MAIN-CHAIN BOND (A**2) : 0.908 ; NULL REMARK 3 MAIN-CHAIN ANGLE (A**2) : 1.222 ; NULL REMARK 3 SIDE-CHAIN BOND (A**2) : 1.301 ; NULL REMARK 3 SIDE-CHAIN ANGLE (A**2) : 1.521 ; NULL REMARK 3 REMARK 3 BULK SOLVENT MODELING. REMARK 3 METHOD USED : NULL REMARK 3 KSOL : NULL REMARK 3 BSOL : NULL REMARK 3 REMARK 3 NCS MODEL : NULL REMARK 3 REMARK 3 NCS RESTRAINTS. RMS SIGMA/WEIGHT REMARK 3 GROUP 1 POSITIONAL (A) : NULL ; NULL REMARK 3 GROUP 1 B-FACTOR (A**2) : NULL ; NULL REMARK 3 REMARK 3 PARAMETER FILE 1 : NULL REMARK 3 TOPOLOGY FILE 1 : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 1YFT COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 06-JAN-05. REMARK 100 THE DEPOSITION ID IS D_1000031464. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 16-JUL-04 REMARK 200 TEMPERATURE (KELVIN) : 200 REMARK 200 PH : 6.2 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) : 0.82653 REMARK 200 MONOCHROMATOR : CURVED CRYSTAL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 315 REMARK 200 INTENSITY-INTEGRATION SOFTWARE : BLU-ICE REMARK 200 DATA SCALING SOFTWARE : SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 24100 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.230 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 (%) : 99.7 REMARK 200 DATA REDUNDANCY : 5.400 REMARK 200 R MERGE (I) : 0.08300 REMARK 200 R SYM (I) : NULL REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 12.0000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.23 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.33 REMARK 200 COMPLETENESS FOR SHELL (%) : 100.0 REMARK 200 DATA REDUNDANCY IN SHELL : 5.40 REMARK 200 R MERGE FOR SHELL (I) : 0.44000 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: FOURIER SYNTHESIS REMARK 200 SOFTWARE USED: CNS REMARK 200 STARTING MODEL: 1RIQ REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 46.00 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.26 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: PEG 5000 MME, NACL, TRIS-CL, TRIS REMARK 280 -BASE, GLYCINE, PH 6.2, VAPOR DIFFUSION, SITTING DROP, REMARK 280 TEMPERATURE 298K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 41 21 2 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 -Y+1/2,X+1/2,Z+1/4 REMARK 290 4555 Y+1/2,-X+1/2,Z+3/4 REMARK 290 5555 -X+1/2,Y+1/2,-Z+1/4 REMARK 290 6555 X+1/2,-Y+1/2,-Z+3/4 REMARK 290 7555 Y,X,-Z REMARK 290 8555 -Y,-X,-Z+1/2 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 86.45250 REMARK 290 SMTRY1 3 0.000000 -1.000000 0.000000 36.95600 REMARK 290 SMTRY2 3 1.000000 0.000000 0.000000 36.95600 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 43.22625 REMARK 290 SMTRY1 4 0.000000 1.000000 0.000000 36.95600 REMARK 290 SMTRY2 4 -1.000000 0.000000 0.000000 36.95600 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 129.67875 REMARK 290 SMTRY1 5 -1.000000 0.000000 0.000000 36.95600 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 36.95600 REMARK 290 SMTRY3 5 0.000000 0.000000 -1.000000 43.22625 REMARK 290 SMTRY1 6 1.000000 0.000000 0.000000 36.95600 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 36.95600 REMARK 290 SMTRY3 6 0.000000 0.000000 -1.000000 129.67875 REMARK 290 SMTRY1 7 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY2 7 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 8 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY2 8 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 8 0.000000 0.000000 -1.000000 86.45250 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 300 REMARK: THE BIOLOGICAL UNIT IS THE ENTIRE ASYMMETRIC UNIT, I.E. ONE REMARK 300 ALANYL-TRNA SYNTHETASE MOLECULE IN COMPLEX WITH ONE GLYCINE REMARK 300 MOLECULE. 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 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 6260 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 35600 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -20.0 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 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT2 2 1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT3 2 0.000000 0.000000 -1.000000 172.90500 REMARK 465 REMARK 465 MISSING RESIDUES REMARK 465 THE FOLLOWING RESIDUES WERE NOT LOCATED IN THE REMARK 465 EXPERIMENT. (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 465 IDENTIFIER; SSSEQ=SEQUENCE NUMBER; I=INSERTION CODE.) REMARK 465 REMARK 465 M RES C SSSEQI REMARK 465 MET A 0 REMARK 465 PHE A 428 REMARK 465 LYS A 429 REMARK 465 VAL A 430 REMARK 465 GLU A 431 REMARK 465 ALA A 432 REMARK 465 LYS A 433 REMARK 465 LYS A 434 REMARK 465 VAL A 435 REMARK 465 LYS A 436 REMARK 465 GLU A 458 REMARK 465 HIS A 459 REMARK 465 HIS A 460 REMARK 465 HIS A 461 REMARK 465 HIS A 462 REMARK 465 HIS A 463 REMARK 465 HIS A 464 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 186 O HOH A 504 2.04 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CLOSE CONTACTS REMARK 500 REMARK 500 THE FOLLOWING ATOMS THAT ARE RELATED BY CRYSTALLOGRAPHIC REMARK 500 SYMMETRY ARE IN CLOSE CONTACT. AN ATOM LOCATED WITHIN 0.15 REMARK 500 ANGSTROMS OF A SYMMETRY RELATED ATOM IS ASSUMED TO BE ON A REMARK 500 SPECIAL POSITION AND IS, THEREFORE, LISTED IN REMARK 375 REMARK 500 INSTEAD OF REMARK 500. ATOMS WITH NON-BLANK ALTERNATE REMARK 500 LOCATION INDICATORS ARE NOT INCLUDED IN THE CALCULATIONS. REMARK 500 REMARK 500 DISTANCE CUTOFF: REMARK 500 2.2 ANGSTROMS FOR CONTACTS NOT INVOLVING HYDROGEN ATOMS REMARK 500 1.6 ANGSTROMS FOR CONTACTS INVOLVING HYDROGEN ATOMS REMARK 500 REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI SSYMOP DISTANCE REMARK 500 ND2 ASN A 48 ND2 ASN A 48 7556 1.18 REMARK 500 N GLY A 72 O GLU A 204 7556 2.11 REMARK 500 CA GLY A 72 O GLU A 204 7556 2.17 REMARK 500 O ASN A 32 O LEU A 51 7556 2.18 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: COVALENT BOND LENGTHS REMARK 500 REMARK 500 THE STEREOCHEMICAL PARAMETERS OF THE FOLLOWING RESIDUES REMARK 500 HAVE VALUES WHICH DEVIATE FROM EXPECTED VALUES BY MORE REMARK 500 THAN 6*RMSD (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 500 IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 STANDARD TABLE: REMARK 500 FORMAT: (10X,I3,1X,2(A3,1X,A1,I4,A1,1X,A4,3X),1X,F6.3) REMARK 500 REMARK 500 EXPECTED VALUES PROTEIN: ENGH AND HUBER, 1999 REMARK 500 EXPECTED VALUES NUCLEIC ACID: CLOWNEY ET AL 1996 REMARK 500 REMARK 500 M RES CSSEQI ATM1 RES CSSEQI ATM2 DEVIATION REMARK 500 ASP A 186 C ASP A 186 O -0.118 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 186 N - CA - CB ANGL. DEV. = -23.3 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 LEU A 2 118.51 71.53 REMARK 500 ASP A 33 58.37 -153.93 REMARK 500 PRO A 34 -0.41 -53.97 REMARK 500 ARG A 69 52.44 -108.16 REMARK 500 SER A 71 142.09 -170.60 REMARK 500 PHE A 98 77.68 -107.54 REMARK 500 ASP A 100 -115.07 -107.76 REMARK 500 PHE A 102 -141.21 -130.13 REMARK 500 MET A 198 92.25 -69.67 REMARK 500 ASP A 203 172.59 -52.64 REMARK 500 ASN A 205 -13.61 -46.95 REMARK 500 SER A 287 -167.55 -173.07 REMARK 500 PHE A 315 -27.19 -149.07 REMARK 500 PHE A 352 -24.73 -147.93 REMARK 500 ASP A 409 96.89 -65.10 REMARK 500 LYS A 426 -82.87 -149.64 REMARK 500 LYS A 443 1.97 84.83 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 GLY A 500 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 1RIQ RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF THE CATALYTIC FRAGMENT OF AQUIFEX AEOLICUS REMARK 900 ALANYL-TRNA SYNTHETASE, APO ENZYME. REMARK 900 RELATED ID: 1YFR RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF THE CATALYTIC FRAGMENT OF A. AEOLICUS ALANLY- REMARK 900 TRNA SYNTHETASE IN COMPLEX WITH ATP AND MAGNESIUM. REMARK 900 RELATED ID: 1YFS RELATED DB: PDB REMARK 900 CRYSTAL SRTUCTURE OF THE CATALYTIC FRAGMENT OF A. AEOLICUS ALANYL- REMARK 900 TRNA SYNTHETASE IN COMPLEX WITH L-ALANINE REMARK 900 RELATED ID: 1YGB RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF THE CATALYTIC FRAGMENT OF ALANYL-TRNA REMARK 900 SYNTHETASE IN COMPLEX WITH L-SERINE DBREF 1YFT A 0 453 UNP O67323 SYA_AQUAE 1 454 SEQADV 1YFT ALA A 454 UNP O67323 CLONING ARTIFACT SEQADV 1YFT ALA A 455 UNP O67323 CLONING ARTIFACT SEQADV 1YFT ALA A 456 UNP O67323 CLONING ARTIFACT SEQADV 1YFT LEU A 457 UNP O67323 CLONING ARTIFACT SEQADV 1YFT GLU A 458 UNP O67323 CLONING ARTIFACT SEQADV 1YFT HIS A 459 UNP O67323 EXPRESSION TAG SEQADV 1YFT HIS A 460 UNP O67323 EXPRESSION TAG SEQADV 1YFT HIS A 461 UNP O67323 EXPRESSION TAG SEQADV 1YFT HIS A 462 UNP O67323 EXPRESSION TAG SEQADV 1YFT HIS A 463 UNP O67323 EXPRESSION TAG SEQADV 1YFT HIS A 464 UNP O67323 EXPRESSION TAG SEQRES 1 A 465 MET SER LEU SER ALA HIS GLU ILE ARG GLU LEU PHE LEU SEQRES 2 A 465 SER PHE PHE GLU LYS LYS GLY HIS THR ARG VAL LYS SER SEQRES 3 A 465 ALA PRO LEU VAL PRO GLU ASN ASP PRO THR LEU LEU PHE SEQRES 4 A 465 VAL ASN ALA GLY MET VAL PRO PHE LYS ASN VAL PHE LEU SEQRES 5 A 465 GLY LEU GLU LYS ARG PRO TYR LYS ARG ALA THR SER CYS SEQRES 6 A 465 GLN LYS CYS LEU ARG VAL SER GLY LYS HIS ASN ASP LEU SEQRES 7 A 465 GLU GLN VAL GLY TYR THR SER ARG HIS HIS THR PHE PHE SEQRES 8 A 465 GLU MET LEU GLY ASN PHE SER PHE GLY ASP TYR PHE LYS SEQRES 9 A 465 LYS GLU ALA ILE GLU TYR ALA TRP GLU PHE VAL THR GLU SEQRES 10 A 465 VAL LEU LYS LEU PRO LYS GLU LYS LEU TYR VAL SER VAL SEQRES 11 A 465 TYR LYS ASP ASP GLU GLU ALA TYR ARG ILE TRP ASN GLU SEQRES 12 A 465 HIS ILE GLY ILE PRO SER GLU ARG ILE TRP ARG LEU GLY SEQRES 13 A 465 GLU GLU ASP ASN PHE TRP GLN MET GLY ASP VAL GLY PRO SEQRES 14 A 465 CYS GLY PRO SER SER GLU ILE TYR VAL ASP ARG GLY GLU SEQRES 15 A 465 GLU TYR GLU GLY ASP GLU ARG TYR LEU GLU ILE TRP ASN SEQRES 16 A 465 LEU VAL PHE MET GLN TYR ASN ARG ASP GLU ASN GLY VAL SEQRES 17 A 465 LEU THR PRO LEU PRO HIS PRO ASN ILE ASP THR GLY MET SEQRES 18 A 465 GLY LEU GLU ARG ILE ALA SER VAL LEU GLN GLY LYS ASN SEQRES 19 A 465 SER ASN PHE GLU ILE ASP ILE ILE PHE PRO LEU ILE GLN SEQRES 20 A 465 PHE GLY GLU GLU VAL SER GLY LYS LYS TYR GLY GLU LYS SEQRES 21 A 465 PHE GLU THR ASP VAL ALA LEU ARG VAL ILE ALA ASP HIS SEQRES 22 A 465 LEU ARG ALA ILE THR PHE ALA ILE SER ASP GLY VAL ILE SEQRES 23 A 465 PRO SER ASN GLU GLY ARG GLY TYR VAL ILE ARG ARG ILE SEQRES 24 A 465 LEU ARG ARG ALA MET ARG PHE GLY TYR LYS LEU GLY ILE SEQRES 25 A 465 GLU ASN PRO PHE LEU TYR LYS GLY VAL ASP LEU VAL VAL SEQRES 26 A 465 ASP ILE MET LYS GLU PRO TYR PRO GLU LEU GLU LEU SER SEQRES 27 A 465 ARG GLU PHE VAL LYS GLY ILE VAL LYS GLY GLU GLU LYS SEQRES 28 A 465 ARG PHE ILE LYS THR LEU LYS ALA GLY MET GLU TYR ILE SEQRES 29 A 465 GLN GLU VAL ILE GLN LYS ALA LEU GLU GLU GLY ARG LYS SEQRES 30 A 465 THR LEU SER GLY LYS GLU VAL PHE THR ALA TYR ASP THR SEQRES 31 A 465 TYR GLY PHE PRO VAL ASP LEU ILE ASP GLU ILE ALA ARG SEQRES 32 A 465 GLU LYS GLY LEU GLY ILE ASP LEU GLU GLY PHE GLN CYS SEQRES 33 A 465 GLU LEU GLU GLU GLN ARG GLU ARG ALA ARG LYS HIS PHE SEQRES 34 A 465 LYS VAL GLU ALA LYS LYS VAL LYS PRO VAL TYR SER HIS SEQRES 35 A 465 LEU LYS GLU LEU GLY LYS THR SER ALA PHE VAL GLY ALA SEQRES 36 A 465 ALA ALA LEU GLU HIS HIS HIS HIS HIS HIS HET GLY A 500 5 HETNAM GLY GLYCINE FORMUL 2 GLY C2 H5 N O2 FORMUL 3 HOH *193(H2 O) HELIX 1 1 SER A 3 LYS A 17 1 15 HELIX 2 2 MET A 43 PRO A 45 5 3 HELIX 3 3 PHE A 46 LEU A 51 1 6 HELIX 4 4 PHE A 102 VAL A 117 1 16 HELIX 5 5 ASP A 133 GLU A 142 1 10 HELIX 6 6 PRO A 147 GLU A 149 5 3 HELIX 7 7 GLY A 155 ASN A 159 1 5 HELIX 8 8 GLU A 184 ARG A 188 1 5 HELIX 9 9 LEU A 222 GLN A 230 1 9 HELIX 10 10 SER A 234 ILE A 238 5 5 HELIX 11 11 ILE A 241 GLY A 253 1 13 HELIX 12 12 LYS A 259 ASP A 282 1 24 HELIX 13 13 GLU A 289 LEU A 309 1 21 HELIX 14 14 PHE A 315 LYS A 328 1 14 HELIX 15 15 GLU A 333 ARG A 351 1 19 HELIX 16 16 PHE A 352 GLU A 373 1 22 HELIX 17 17 SER A 379 THR A 389 1 11 HELIX 18 18 PRO A 393 GLU A 403 1 11 HELIX 19 19 ASP A 409 ARG A 425 1 17 HELIX 20 20 GLU A 444 SER A 449 1 6 SHEET 1 A 8 THR A 21 ARG A 22 0 SHEET 2 A 8 ARG A 60 LEU A 68 1 O ARG A 60 N THR 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 LEU A 208 GLY A 221 -1 O MET A 220 N LEU A 93 SHEET 5 A 8 TYR A 189 ARG A 202 -1 N ASN A 201 O THR A 209 SHEET 6 A 8 GLY A 167 ASP A 178 -1 N CYS A 169 O TYR A 200 SHEET 7 A 8 LEU A 125 TYR A 130 -1 N TYR A 126 O TYR A 176 SHEET 8 A 8 ILE A 151 LEU A 154 1 O TRP A 152 N VAL A 129 SHEET 1 B 7 THR A 21 ARG A 22 0 SHEET 2 B 7 ARG A 60 LEU A 68 1 O ARG A 60 N THR 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 LEU A 208 GLY A 221 -1 O MET A 220 N LEU A 93 SHEET 5 B 7 TYR A 189 ARG A 202 -1 N ASN A 201 O THR A 209 SHEET 6 B 7 GLY A 167 ASP A 178 -1 N CYS A 169 O TYR A 200 SHEET 7 B 7 PHE A 160 GLN A 162 -1 N TRP A 161 O GLY A 170 SHEET 1 C 2 VAL A 70 SER A 71 0 SHEET 2 C 2 HIS A 74 ASN A 75 -1 O HIS A 74 N SER A 71 SHEET 1 D 2 THR A 377 LEU A 378 0 SHEET 2 D 2 GLY A 407 ILE A 408 1 O GLY A 407 N LEU A 378 SITE 1 AC1 5 MET A 92 ASN A 194 ASP A 217 HOH A 501 SITE 2 AC1 5 HOH A 681 CRYST1 73.912 73.912 172.905 90.00 90.00 90.00 P 41 21 2 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 0.013530 0.000000 0.000000 0.00000 SCALE2 0.000000 0.013530 0.000000 0.00000 SCALE3 0.000000 0.000000 0.005784 0.00000