HEADER TRANSLATION 18-JUL-18 6AAC
TITLE CRYSTAL STRUCTURE OF METHANOSARCINA MAZEI PYLRS(Y306A/Y384F) COMPLEXED
TITLE 2 WITH MAZZLYS
COMPND MOL_ID: 1;
COMPND 2 MOLECULE: PYRROLYSINE--TRNA LIGASE;
COMPND 3 CHAIN: A;
COMPND 4 SYNONYM: PYRROLYSINE--TRNA(PYL) LIGASE,PYRROLYSYL-TRNA SYNTHETASE,
COMPND 5 PYLRS;
COMPND 6 EC: 6.1.1.26;
COMPND 7 ENGINEERED: YES;
COMPND 8 MUTATION: YES
SOURCE MOL_ID: 1;
SOURCE 2 ORGANISM_SCIENTIFIC: METHANOSARCINA MAZEI JCM 9314;
SOURCE 3 ORGANISM_COMMON: METHANOSARCINA FRISIA;
SOURCE 4 ORGANISM_TAXID: 1293038;
SOURCE 5 GENE: PYLS;
SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21(DE3);
SOURCE 7 EXPRESSION_SYSTEM_TAXID: 469008;
SOURCE 8 EXPRESSION_SYSTEM_VARIANT: ROSETTA
KEYWDS AMINOACYL-TRNA SYNTHETASE, NON-NATURAL AMINO ACIDS, TRANSLATION
EXPDTA X-RAY DIFFRACTION
AUTHOR T.YANAGISAWA,M.KURATANI,S.YOKOYAMA
REVDAT 4 22-NOV-23 6AAC 1 LINK
REVDAT 3 07-AUG-19 6AAC 1 JRNL
REVDAT 2 22-MAY-19 6AAC 1 SOURCE JRNL
REVDAT 1 17-APR-19 6AAC 0
JRNL AUTH T.YANAGISAWA,M.KURATANI,E.SEKI,N.HINO,K.SAKAMOTO,S.YOKOYAMA
JRNL TITL STRUCTURAL BASIS FOR GENETIC-CODE EXPANSION WITH BULKY
JRNL TITL 2 LYSINE DERIVATIVES BY AN ENGINEERED PYRROLYSYL-TRNA
JRNL TITL 3 SYNTHETASE.
JRNL REF CELL CHEM BIOL V. 26 936 2019
JRNL REFN ESSN 2451-9456
JRNL PMID 31031143
JRNL DOI 10.1016/J.CHEMBIOL.2019.03.008
REMARK 2
REMARK 2 RESOLUTION. 1.48 ANGSTROMS.
REMARK 3
REMARK 3 REFINEMENT.
REMARK 3 PROGRAM : PHENIX (1.10.1_2155: ???)
REMARK 3 AUTHORS : PAUL ADAMS,PAVEL AFONINE,VINCENT CHEN,IAN
REMARK 3 : DAVIS,KRESHNA GOPAL,RALF GROSSE-KUNSTLEVE,
REMARK 3 : LI-WEI HUNG,ROBERT IMMORMINO,TOM IOERGER,
REMARK 3 : AIRLIE MCCOY,ERIK MCKEE,NIGEL MORIARTY,
REMARK 3 : REETAL PAI,RANDY READ,JANE RICHARDSON,
REMARK 3 : DAVID RICHARDSON,TOD ROMO,JIM SACCHETTINI,
REMARK 3 : NICHOLAS SAUTER,JACOB SMITH,LAURENT
REMARK 3 : STORONI,TOM TERWILLIGER,PETER ZWART
REMARK 3
REMARK 3 REFINEMENT TARGET : ML
REMARK 3
REMARK 3 DATA USED IN REFINEMENT.
REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.48
REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 35.05
REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.410
REMARK 3 COMPLETENESS FOR RANGE (%) : 99.5
REMARK 3 NUMBER OF REFLECTIONS : 47308
REMARK 3
REMARK 3 FIT TO DATA USED IN REFINEMENT.
REMARK 3 R VALUE (WORKING + TEST SET) : 0.143
REMARK 3 R VALUE (WORKING SET) : 0.142
REMARK 3 FREE R VALUE : 0.182
REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.230
REMARK 3 FREE R VALUE TEST SET COUNT : 2000
REMARK 3
REMARK 3 FIT TO DATA USED IN REFINEMENT (IN BINS).
REMARK 3 BIN RESOLUTION RANGE COMPL. NWORK NFREE RWORK RFREE
REMARK 3 1 35.0588 - 3.5644 0.97 3279 145 0.1596 0.1868
REMARK 3 2 3.5644 - 2.8296 1.00 3293 145 0.1540 0.1868
REMARK 3 3 2.8296 - 2.4720 1.00 3252 144 0.1605 0.1815
REMARK 3 4 2.4720 - 2.2460 1.00 3265 144 0.1365 0.1730
REMARK 3 5 2.2460 - 2.0851 1.00 3258 144 0.1249 0.1733
REMARK 3 6 2.0851 - 1.9622 1.00 3250 143 0.1257 0.1746
REMARK 3 7 1.9622 - 1.8639 1.00 3244 143 0.1249 0.2010
REMARK 3 8 1.8639 - 1.7828 1.00 3219 142 0.1258 0.1816
REMARK 3 9 1.7828 - 1.7141 1.00 3246 144 0.1209 0.1673
REMARK 3 10 1.7141 - 1.6550 1.00 3226 142 0.1130 0.1631
REMARK 3 11 1.6550 - 1.6032 1.00 3218 142 0.1152 0.1763
REMARK 3 12 1.6032 - 1.5574 1.00 3237 143 0.1136 0.1827
REMARK 3 13 1.5574 - 1.5164 0.99 3188 141 0.1146 0.2003
REMARK 3 14 1.5164 - 1.4794 0.97 3133 138 0.1324 0.1802
REMARK 3
REMARK 3 BULK SOLVENT MODELLING.
REMARK 3 METHOD USED : FLAT BULK SOLVENT MODEL
REMARK 3 SOLVENT RADIUS : 1.11
REMARK 3 SHRINKAGE RADIUS : 0.90
REMARK 3 K_SOL : NULL
REMARK 3 B_SOL : NULL
REMARK 3
REMARK 3 ERROR ESTIMATES.
REMARK 3 COORDINATE ERROR (MAXIMUM-LIKELIHOOD BASED) : 0.110
REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 16.540
REMARK 3
REMARK 3 B VALUES.
REMARK 3 FROM WILSON PLOT (A**2) : NULL
REMARK 3 MEAN B VALUE (OVERALL, A**2) : NULL
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 TWINNING INFORMATION.
REMARK 3 FRACTION: NULL
REMARK 3 OPERATOR: NULL
REMARK 3
REMARK 3 DEVIATIONS FROM IDEAL VALUES.
REMARK 3 RMSD COUNT
REMARK 3 BOND : 0.014 2365
REMARK 3 ANGLE : 1.434 3203
REMARK 3 CHIRALITY : 0.104 343
REMARK 3 PLANARITY : 0.009 413
REMARK 3 DIHEDRAL : 17.090 951
REMARK 3
REMARK 3 TLS DETAILS
REMARK 3 NUMBER OF TLS GROUPS : NULL
REMARK 3
REMARK 3 NCS DETAILS
REMARK 3 NUMBER OF NCS GROUPS : NULL
REMARK 3
REMARK 3 OTHER REFINEMENT REMARKS: NULL
REMARK 4
REMARK 4 6AAC COMPLIES WITH FORMAT V. 3.30, 13-JUL-11
REMARK 100
REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 31-JUL-18.
REMARK 100 THE DEPOSITION ID IS D_1300008409.
REMARK 200
REMARK 200 EXPERIMENTAL DETAILS
REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION
REMARK 200 DATE OF DATA COLLECTION : 13-JUL-14
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 : SPRING-8
REMARK 200 BEAMLINE : BL32XU
REMARK 200 X-RAY GENERATOR MODEL : NULL
REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M
REMARK 200 WAVELENGTH OR RANGE (A) : 1
REMARK 200 MONOCHROMATOR : NULL
REMARK 200 OPTICS : NULL
REMARK 200
REMARK 200 DETECTOR TYPE : CCD
REMARK 200 DETECTOR MANUFACTURER : RAYONIX MX225-HS
REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS
REMARK 200 DATA SCALING SOFTWARE : XSCALE
REMARK 200
REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 47308
REMARK 200 RESOLUTION RANGE HIGH (A) : 1.480
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 (%) : 99.6
REMARK 200 DATA REDUNDANCY : 4.100
REMARK 200 R MERGE (I) : NULL
REMARK 200 R SYM (I) : NULL
REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 16.5000
REMARK 200
REMARK 200 IN THE HIGHEST RESOLUTION SHELL.
REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.48
REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.52
REMARK 200 COMPLETENESS FOR SHELL (%) : NULL
REMARK 200 DATA REDUNDANCY IN SHELL : NULL
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: PHASER
REMARK 200 STARTING MODEL: 2ZIM
REMARK 200
REMARK 200 REMARK: NULL
REMARK 280
REMARK 280 CRYSTAL
REMARK 280 SOLVENT CONTENT, VS (%): 46.13
REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.28
REMARK 280
REMARK 280 CRYSTALLIZATION CONDITIONS: 100MM TRIS-HCL BUFFER (PH 8.5), 40%
REMARK 280 PEG 200, 200MM KCL, 40MM MGCL2, 10MM SODIUM CITRATE, VAPOR
REMARK 280 DIFFUSION, HANGING DROP, TEMPERATURE 281K
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 50.74600
REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 22.14200
REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 0.00000
REMARK 290 SMTRY1 4 -1.000000 0.000000 0.000000 50.74600
REMARK 290 SMTRY2 4 0.000000 1.000000 0.000000 22.14200
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: DIMERIC
REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC
REMARK 350 SOFTWARE USED: PISA
REMARK 350 TOTAL BURIED SURFACE AREA: 8280 ANGSTROM**2
REMARK 350 SURFACE AREA OF THE COMPLEX: 22520 ANGSTROM**2
REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -69.0 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 168.33576
REMARK 350 BIOMT2 2 0.000000 1.000000 0.000000 0.00000
REMARK 350 BIOMT3 2 0.000000 0.000000 -1.000000 63.84069
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 GLY A 181
REMARK 465 SER A 182
REMARK 465 HIS A 183
REMARK 465 MET A 184
REMARK 465 ALA A 185
REMARK 465 SER A 186
REMARK 465 ALA A 187
REMARK 465 ASP A 281
REMARK 465 THR A 282
REMARK 465 GLU A 283
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 NH2 ARG A 409 O HOH A 601 2.14
REMARK 500 O HOH A 690 O HOH A 826 2.14
REMARK 500 O ASN A 280 O HOH A 602 2.14
REMARK 500 O HOH A 849 O HOH A 867 2.16
REMARK 500 O HOH A 731 O HOH A 864 2.17
REMARK 500 O HOH A 734 O HOH A 815 2.18
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 GLU A 238 -64.82 -120.94
REMARK 500 ASP A 292 -137.27 59.01
REMARK 500
REMARK 500 REMARK: NULL
REMARK 525
REMARK 525 SOLVENT
REMARK 525
REMARK 525 THE SOLVENT MOLECULES HAVE CHAIN IDENTIFIERS THAT
REMARK 525 INDICATE THE POLYMER CHAIN WITH WHICH THEY ARE MOST
REMARK 525 CLOSELY ASSOCIATED. THE REMARK LISTS ALL THE SOLVENT
REMARK 525 MOLECULES WHICH ARE MORE THAN 5A AWAY FROM THE
REMARK 525 NEAREST POLYMER CHAIN (M = MODEL NUMBER;
REMARK 525 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE
REMARK 525 NUMBER; I=INSERTION CODE):
REMARK 525
REMARK 525 M RES CSSEQI
REMARK 525 HOH A 925 DISTANCE = 6.01 ANGSTROMS
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 K A 506 K
REMARK 620 N RES CSSEQI ATOM
REMARK 620 1 ASN A 203 O
REMARK 620 2 ASP A 206 O 87.0
REMARK 620 3 HOH A 610 O 106.8 50.1
REMARK 620 4 HOH A 798 O 126.9 66.9 91.1
REMARK 620 5 HOH A 865 O 86.0 158.7 113.4 132.3
REMARK 620 N 1 2 3 4
REMARK 620
REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL
REMARK 620 MG A 502 MG
REMARK 620 N RES CSSEQI ATOM
REMARK 620 1 GLU A 396 OE2
REMARK 620 2 SER A 399 OG 92.4
REMARK 620 3 ATP A 504 O1A 96.1 94.3
REMARK 620 4 ATP A 504 O1B 91.1 172.4 92.1
REMARK 620 5 HOH A 643 O 90.5 87.5 173.1 85.7
REMARK 620 6 HOH A 750 O 177.5 88.5 86.2 87.8 87.2
REMARK 620 N 1 2 3 4 5
REMARK 620
REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL
REMARK 620 MG A 503 MG
REMARK 620 N RES CSSEQI ATOM
REMARK 620 1 GLU A 396 OE1
REMARK 620 2 ATP A 504 O1G 92.0
REMARK 620 3 ATP A 504 O1B 92.9 87.4
REMARK 620 4 HOH A 643 O 76.6 161.2 78.5
REMARK 620 5 HOH A 804 O 174.9 93.0 86.3 98.4
REMARK 620 6 HOH A 813 O 87.1 98.0 174.6 96.3 93.2
REMARK 620 N 1 2 3 4 5
REMARK 620
REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL
REMARK 620 MG A 501 MG
REMARK 620 N RES CSSEQI ATOM
REMARK 620 1 ATP A 504 O2B
REMARK 620 2 ATP A 504 O2G 90.4
REMARK 620 3 HOH A 654 O 92.8 93.4
REMARK 620 4 HOH A 664 O 179.1 90.1 86.3
REMARK 620 5 HOH A 723 O 86.9 177.0 87.9 92.7
REMARK 620 6 HOH A 733 O 92.2 86.0 174.9 88.6 93.0
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 501
REMARK 800
REMARK 800 SITE_IDENTIFIER: AC2
REMARK 800 EVIDENCE_CODE: SOFTWARE
REMARK 800 SITE_DESCRIPTION: binding site for residue MG A 502
REMARK 800
REMARK 800 SITE_IDENTIFIER: AC3
REMARK 800 EVIDENCE_CODE: SOFTWARE
REMARK 800 SITE_DESCRIPTION: binding site for residue MG A 503
REMARK 800
REMARK 800 SITE_IDENTIFIER: AC4
REMARK 800 EVIDENCE_CODE: SOFTWARE
REMARK 800 SITE_DESCRIPTION: binding site for residue ATP A 504
REMARK 800
REMARK 800 SITE_IDENTIFIER: AC5
REMARK 800 EVIDENCE_CODE: SOFTWARE
REMARK 800 SITE_DESCRIPTION: binding site for residue 9TR A 505
REMARK 800
REMARK 800 SITE_IDENTIFIER: AC6
REMARK 800 EVIDENCE_CODE: SOFTWARE
REMARK 800 SITE_DESCRIPTION: binding site for residue K A 506
REMARK 800
REMARK 800 SITE_IDENTIFIER: AC7
REMARK 800 EVIDENCE_CODE: SOFTWARE
REMARK 800 SITE_DESCRIPTION: binding site for residue PEG A 507
REMARK 800
REMARK 800 SITE_IDENTIFIER: AC8
REMARK 800 EVIDENCE_CODE: SOFTWARE
REMARK 800 SITE_DESCRIPTION: binding site for residue PGE A 508
REMARK 999
REMARK 999 SEQUENCE
REMARK 999 THE SEQUENCE REFERENCE Q8PWY1 (PYLS_METMA) IS DERIVED FROM A
REMARK 999 DIFFERENT STRAIN (METHANOSARCINA MAZEI GO1, TAXID 192952). RESIDUE
REMARK 999 E444G IS A NATURAL MUTATION OBSERVED IN PYLRS GENE FROM
REMARK 999 METHANOSARCINA MAZEI JCM 9314 GENOME.
DBREF 6AAC A 185 454 UNP Q8PWY1 PYLS_METMA 185 454
SEQADV 6AAC GLY A 181 UNP Q8PWY1 EXPRESSION TAG
SEQADV 6AAC SER A 182 UNP Q8PWY1 EXPRESSION TAG
SEQADV 6AAC HIS A 183 UNP Q8PWY1 EXPRESSION TAG
SEQADV 6AAC MET A 184 UNP Q8PWY1 EXPRESSION TAG
SEQADV 6AAC ALA A 306 UNP Q8PWY1 TYR 306 ENGINEERED MUTATION
SEQADV 6AAC PHE A 384 UNP Q8PWY1 TYR 384 ENGINEERED MUTATION
SEQADV 6AAC GLY A 444 UNP Q8PWY1 GLU 444 SEE SEQUENCE DETAILS
SEQRES 1 A 274 GLY SER HIS MET ALA SER ALA PRO ALA LEU THR LYS SER
SEQRES 2 A 274 GLN THR ASP ARG LEU GLU VAL LEU LEU ASN PRO LYS ASP
SEQRES 3 A 274 GLU ILE SER LEU ASN SER GLY LYS PRO PHE ARG GLU LEU
SEQRES 4 A 274 GLU SER GLU LEU LEU SER ARG ARG LYS LYS ASP LEU GLN
SEQRES 5 A 274 GLN ILE TYR ALA GLU GLU ARG GLU ASN TYR LEU GLY LYS
SEQRES 6 A 274 LEU GLU ARG GLU ILE THR ARG PHE PHE VAL ASP ARG GLY
SEQRES 7 A 274 PHE LEU GLU ILE LYS SER PRO ILE LEU ILE PRO LEU GLU
SEQRES 8 A 274 TYR ILE GLU ARG MET GLY ILE ASP ASN ASP THR GLU LEU
SEQRES 9 A 274 SER LYS GLN ILE PHE ARG VAL ASP LYS ASN PHE CYS LEU
SEQRES 10 A 274 ARG PRO MET LEU ALA PRO ASN LEU ALA ASN TYR LEU ARG
SEQRES 11 A 274 LYS LEU ASP ARG ALA LEU PRO ASP PRO ILE LYS ILE PHE
SEQRES 12 A 274 GLU ILE GLY PRO CYS TYR ARG LYS GLU SER ASP GLY LYS
SEQRES 13 A 274 GLU HIS LEU GLU GLU PHE THR MET LEU ASN PHE CYS GLN
SEQRES 14 A 274 MET GLY SER GLY CYS THR ARG GLU ASN LEU GLU SER ILE
SEQRES 15 A 274 ILE THR ASP PHE LEU ASN HIS LEU GLY ILE ASP PHE LYS
SEQRES 16 A 274 ILE VAL GLY ASP SER CYS MET VAL PHE GLY ASP THR LEU
SEQRES 17 A 274 ASP VAL MET HIS GLY ASP LEU GLU LEU SER SER ALA VAL
SEQRES 18 A 274 VAL GLY PRO ILE PRO LEU ASP ARG GLU TRP GLY ILE ASP
SEQRES 19 A 274 LYS PRO TRP ILE GLY ALA GLY PHE GLY LEU GLU ARG LEU
SEQRES 20 A 274 LEU LYS VAL LYS HIS ASP PHE LYS ASN ILE LYS ARG ALA
SEQRES 21 A 274 ALA ARG SER GLY SER TYR TYR ASN GLY ILE SER THR ASN
SEQRES 22 A 274 LEU
HET MG A 501 1
HET MG A 502 1
HET MG A 503 1
HET ATP A 504 31
HET 9TR A 505 23
HET K A 506 1
HET PEG A 507 7
HET PGE A 508 10
HETNAM MG MAGNESIUM ION
HETNAM ATP ADENOSINE-5'-TRIPHOSPHATE
HETNAM 9TR N6-{[(3-AZIDOPHENYL)METHOXY]CARBONYL}-L-LYSINE
HETNAM K POTASSIUM ION
HETNAM PEG DI(HYDROXYETHYL)ETHER
HETNAM PGE TRIETHYLENE GLYCOL
FORMUL 2 MG 3(MG 2+)
FORMUL 5 ATP C10 H16 N5 O13 P3
FORMUL 6 9TR C14 H19 N5 O4
FORMUL 7 K K 1+
FORMUL 8 PEG C4 H10 O3
FORMUL 9 PGE C6 H14 O4
FORMUL 10 HOH *325(H2 O)
HELIX 1 AA1 THR A 191 LEU A 202 1 12
HELIX 2 AA2 PRO A 215 GLU A 238 1 24
HELIX 3 AA3 ASN A 241 ARG A 257 1 17
HELIX 4 AA4 LEU A 270 MET A 276 1 7
HELIX 5 AA5 LEU A 284 ILE A 288 5 5
HELIX 6 AA6 LEU A 301 ASP A 313 1 13
HELIX 7 AA7 THR A 355 GLY A 371 1 17
HELIX 8 AA8 ILE A 405 GLY A 412 5 8
HELIX 9 AA9 LEU A 424 ASP A 433 1 10
HELIX 10 AB1 ASN A 436 ALA A 441 5 6
SHEET 1 AA1 7 LEU A 260 ILE A 262 0
SHEET 2 AA1 7 ILE A 320 TYR A 329 1 O PHE A 323 N ILE A 262
SHEET 3 AA1 7 GLU A 341 MET A 350 -1 O MET A 344 N GLY A 326
SHEET 4 AA1 7 TRP A 417 GLY A 423 -1 O PHE A 422 N LEU A 345
SHEET 5 AA1 7 LEU A 395 VAL A 402 -1 N VAL A 401 O GLY A 419
SHEET 6 AA1 7 GLY A 385 HIS A 392 -1 N HIS A 392 O LEU A 395
SHEET 7 AA1 7 LYS A 375 CYS A 381 -1 N LYS A 375 O MET A 391
SHEET 1 AA2 3 LEU A 267 PRO A 269 0
SHEET 2 AA2 3 PHE A 295 LEU A 297 -1 O CYS A 296 N ILE A 268
SHEET 3 AA2 3 ARG A 290 VAL A 291 -1 N VAL A 291 O PHE A 295
SHEET 1 AA3 2 TYR A 446 TYR A 447 0
SHEET 2 AA3 2 ILE A 450 SER A 451 -1 O ILE A 450 N TYR A 447
LINK O ASN A 203 K K A 506 1555 1555 2.88
LINK O ASP A 206 K K A 506 1555 1555 2.99
LINK OE2 GLU A 396 MG MG A 502 1555 1555 2.17
LINK OE1 GLU A 396 MG MG A 503 1555 1555 2.31
LINK OG SER A 399 MG MG A 502 1555 1555 2.10
LINK MG MG A 501 O2B ATP A 504 1555 1555 2.05
LINK MG MG A 501 O2G ATP A 504 1555 1555 2.11
LINK MG MG A 501 O HOH A 654 1555 1555 2.12
LINK MG MG A 501 O HOH A 664 1555 1555 2.13
LINK MG MG A 501 O HOH A 723 1555 1555 2.07
LINK MG MG A 501 O HOH A 733 1555 1555 2.08
LINK MG MG A 502 O1A ATP A 504 1555 1555 2.12
LINK MG MG A 502 O1B ATP A 504 1555 1555 2.14
LINK MG MG A 502 O HOH A 643 1555 1555 2.15
LINK MG MG A 502 O HOH A 750 1555 1555 2.12
LINK MG MG A 503 O1G ATP A 504 1555 1555 2.24
LINK MG MG A 503 O1B ATP A 504 1555 1555 2.29
LINK MG MG A 503 O HOH A 643 1555 1555 2.32
LINK MG MG A 503 O HOH A 804 1555 1555 2.17
LINK MG MG A 503 O HOH A 813 1555 1555 2.16
LINK K K A 506 O HOH A 610 1555 1555 2.55
LINK K K A 506 O HOH A 798 1555 1555 2.95
LINK K K A 506 O HOH A 865 1555 1555 2.89
CISPEP 1 ASP A 318 PRO A 319 0 -1.79
CISPEP 2 GLY A 403 PRO A 404 0 2.53
SITE 1 AC1 5 ATP A 504 HOH A 654 HOH A 664 HOH A 723
SITE 2 AC1 5 HOH A 733
SITE 1 AC2 6 GLU A 396 SER A 399 MG A 503 ATP A 504
SITE 2 AC2 6 HOH A 643 HOH A 750
SITE 1 AC3 6 GLU A 396 MG A 502 ATP A 504 HOH A 643
SITE 2 AC3 6 HOH A 804 HOH A 813
SITE 1 AC4 29 ARG A 330 GLU A 332 HIS A 338 LEU A 339
SITE 2 AC4 29 PHE A 342 MET A 344 GLU A 396 LEU A 397
SITE 3 AC4 29 SER A 398 SER A 399 GLY A 421 GLY A 423
SITE 4 AC4 29 ARG A 426 MG A 501 MG A 502 MG A 503
SITE 5 AC4 29 9TR A 505 HOH A 643 HOH A 654 HOH A 664
SITE 6 AC4 29 HOH A 666 HOH A 723 HOH A 728 HOH A 733
SITE 7 AC4 29 HOH A 750 HOH A 767 HOH A 772 HOH A 800
SITE 8 AC4 29 HOH A 804
SITE 1 AC5 13 MET A 276 ALA A 302 ALA A 306 LEU A 309
SITE 2 AC5 13 ASN A 346 PHE A 384 SER A 399 LEU A 407
SITE 3 AC5 13 ASP A 408 ILE A 413 TRP A 417 ATP A 504
SITE 4 AC5 13 HOH A 802
SITE 1 AC6 6 ASN A 203 PRO A 204 ASP A 206 HOH A 610
SITE 2 AC6 6 HOH A 798 HOH A 865
SITE 1 AC7 8 SER A 333 ASP A 334 GLY A 335 LYS A 336
SITE 2 AC7 8 GLU A 337 HIS A 338 PGE A 508 HOH A 663
SITE 1 AC8 7 LEU A 370 GLY A 371 VAL A 430 LYS A 431
SITE 2 AC8 7 ASP A 433 PEG A 507 HOH A 628
CRYST1 101.492 44.284 72.637 90.00 118.49 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 0.009853 0.000000 0.005348 0.00000
SCALE2 0.000000 0.022582 0.000000 0.00000
SCALE3 0.000000 0.000000 0.015664 0.00000