HEADER TRANSLATION 18-JUL-18 6AAP
TITLE CRYSTAL STRUCTURE OF METHANOSARCINA MAZEI PYLRS(Y306A/Y384F) COMPLEXED
TITLE 2 WITH ZAESECYS
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 6AAP 1 LINK
REVDAT 3 07-AUG-19 6AAP 1 JRNL
REVDAT 2 22-MAY-19 6AAP 1 SOURCE JRNL
REVDAT 1 17-APR-19 6AAP 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. 1.50 ANGSTROMS.
REMARK 3
REMARK 3 REFINEMENT.
REMARK 3 PROGRAM : PHENIX (1.13_2998: ???)
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 : NULL
REMARK 3
REMARK 3 DATA USED IN REFINEMENT.
REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.50
REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 37.04
REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.350
REMARK 3 COMPLETENESS FOR RANGE (%) : 99.6
REMARK 3 NUMBER OF REFLECTIONS : 43991
REMARK 3
REMARK 3 FIT TO DATA USED IN REFINEMENT.
REMARK 3 R VALUE (WORKING + TEST SET) : 0.165
REMARK 3 R VALUE (WORKING SET) : 0.164
REMARK 3 FREE R VALUE : 0.196
REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.040
REMARK 3 FREE R VALUE TEST SET COUNT : 2217
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 37.0519 - 3.7755 1.00 2735 134 0.1509 0.1858
REMARK 3 2 3.7755 - 2.9971 1.00 2659 139 0.1510 0.2057
REMARK 3 3 2.9971 - 2.6184 1.00 2620 146 0.1698 0.1926
REMARK 3 4 2.6184 - 2.3790 1.00 2619 164 0.1772 0.1806
REMARK 3 5 2.3790 - 2.2085 1.00 2594 153 0.1673 0.1910
REMARK 3 6 2.2085 - 2.0783 1.00 2657 110 0.1638 0.1874
REMARK 3 7 2.0783 - 1.9742 1.00 2618 124 0.1684 0.2025
REMARK 3 8 1.9742 - 1.8883 1.00 2586 141 0.1674 0.2071
REMARK 3 9 1.8883 - 1.8156 1.00 2620 146 0.1676 0.2146
REMARK 3 10 1.8156 - 1.7530 1.00 2591 141 0.1731 0.2081
REMARK 3 11 1.7530 - 1.6982 0.99 2592 145 0.1790 0.2177
REMARK 3 12 1.6982 - 1.6496 0.99 2591 128 0.1740 0.1893
REMARK 3 13 1.6496 - 1.6062 0.99 2602 122 0.1703 0.1992
REMARK 3 14 1.6062 - 1.5670 0.99 2566 139 0.1798 0.2036
REMARK 3 15 1.5670 - 1.5314 0.99 2580 133 0.1877 0.2254
REMARK 3 16 1.5314 - 1.4988 0.98 2544 152 0.1955 0.2309
REMARK 3
REMARK 3 BULK SOLVENT MODELLING.
REMARK 3 METHOD USED : NULL
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) : 0.130
REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 19.180
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 : 0.005 2320
REMARK 3 ANGLE : 0.948 3139
REMARK 3 CHIRALITY : 0.079 338
REMARK 3 PLANARITY : 0.006 405
REMARK 3 DIHEDRAL : 17.613 918
REMARK 3
REMARK 3 TLS DETAILS
REMARK 3 NUMBER OF TLS GROUPS : 5
REMARK 3 TLS GROUP : 1
REMARK 3 SELECTION: CHAIN 'A' AND (RESID 188 THROUGH 215 )
REMARK 3 ORIGIN FOR THE GROUP (A): 4.4997 28.7485 50.5386
REMARK 3 T TENSOR
REMARK 3 T11: 0.1869 T22: 0.2935
REMARK 3 T33: 0.2201 T12: 0.0250
REMARK 3 T13: 0.0012 T23: 0.0027
REMARK 3 L TENSOR
REMARK 3 L11: 1.2342 L22: 3.9698
REMARK 3 L33: 2.8245 L12: -0.3949
REMARK 3 L13: -0.5066 L23: 1.3015
REMARK 3 S TENSOR
REMARK 3 S11: -0.0558 S12: 0.1421 S13: -0.1512
REMARK 3 S21: -0.0772 S22: -0.0690 S23: 0.2716
REMARK 3 S31: 0.1855 S32: -0.3946 S33: 0.0988
REMARK 3 TLS GROUP : 2
REMARK 3 SELECTION: CHAIN 'A' AND (RESID 216 THROUGH 256 )
REMARK 3 ORIGIN FOR THE GROUP (A): 19.7921 18.8361 43.5676
REMARK 3 T TENSOR
REMARK 3 T11: 0.1766 T22: 0.1729
REMARK 3 T33: 0.1637 T12: -0.0051
REMARK 3 T13: 0.0142 T23: 0.0050
REMARK 3 L TENSOR
REMARK 3 L11: 0.5551 L22: 0.0646
REMARK 3 L33: 0.9775 L12: -0.0705
REMARK 3 L13: -0.5771 L23: -0.1069
REMARK 3 S TENSOR
REMARK 3 S11: -0.1435 S12: -0.0667 S13: -0.0846
REMARK 3 S21: 0.1047 S22: 0.0095 S23: 0.0352
REMARK 3 S31: 0.1969 S32: -0.1384 S33: 0.1719
REMARK 3 TLS GROUP : 3
REMARK 3 SELECTION: CHAIN 'A' AND (RESID 257 THROUGH 329 )
REMARK 3 ORIGIN FOR THE GROUP (A): 31.2354 34.4136 18.5015
REMARK 3 T TENSOR
REMARK 3 T11: 0.1858 T22: 0.1221
REMARK 3 T33: 0.1671 T12: -0.0060
REMARK 3 T13: -0.0156 T23: 0.0327
REMARK 3 L TENSOR
REMARK 3 L11: 1.5366 L22: 0.8219
REMARK 3 L33: 1.6293 L12: -0.1892
REMARK 3 L13: -0.3168 L23: 0.6536
REMARK 3 S TENSOR
REMARK 3 S11: -0.0198 S12: 0.2012 S13: 0.2762
REMARK 3 S21: -0.1963 S22: -0.0126 S23: -0.0365
REMARK 3 S31: -0.3184 S32: -0.0778 S33: 0.0349
REMARK 3 TLS GROUP : 4
REMARK 3 SELECTION: CHAIN 'A' AND (RESID 330 THROUGH 370 )
REMARK 3 ORIGIN FOR THE GROUP (A): 19.9462 25.9457 19.9917
REMARK 3 T TENSOR
REMARK 3 T11: 0.1046 T22: 0.1412
REMARK 3 T33: 0.1459 T12: 0.0076
REMARK 3 T13: -0.0066 T23: 0.0109
REMARK 3 L TENSOR
REMARK 3 L11: 1.5026 L22: 1.4028
REMARK 3 L33: 1.5888 L12: 1.0946
REMARK 3 L13: 0.4793 L23: 0.3084
REMARK 3 S TENSOR
REMARK 3 S11: -0.0748 S12: 0.0662 S13: 0.0805
REMARK 3 S21: -0.0063 S22: -0.0107 S23: 0.1163
REMARK 3 S31: 0.0598 S32: -0.1992 S33: 0.1067
REMARK 3 TLS GROUP : 5
REMARK 3 SELECTION: CHAIN 'A' AND (RESID 371 THROUGH 454 )
REMARK 3 ORIGIN FOR THE GROUP (A): 17.9412 28.5667 23.5385
REMARK 3 T TENSOR
REMARK 3 T11: 0.1317 T22: 0.1467
REMARK 3 T33: 0.1670 T12: 0.0101
REMARK 3 T13: -0.0060 T23: 0.0056
REMARK 3 L TENSOR
REMARK 3 L11: 1.0844 L22: 0.4860
REMARK 3 L33: 1.4594 L12: 0.1610
REMARK 3 L13: -0.0665 L23: 0.0360
REMARK 3 S TENSOR
REMARK 3 S11: -0.0713 S12: 0.0784 S13: 0.1265
REMARK 3 S21: -0.0404 S22: 0.0248 S23: 0.0592
REMARK 3 S31: -0.0779 S32: -0.2353 S33: 0.0072
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 6AAP COMPLIES WITH FORMAT V. 3.30, 13-JUL-11
REMARK 100
REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 01-AUG-18.
REMARK 100 THE DEPOSITION ID IS D_1300008430.
REMARK 200
REMARK 200 EXPERIMENTAL DETAILS
REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION
REMARK 200 DATE OF DATA COLLECTION : 28-NOV-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 : BL26B2
REMARK 200 X-RAY GENERATOR MODEL : NULL
REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M
REMARK 200 WAVELENGTH OR RANGE (A) : 0.97916
REMARK 200 MONOCHROMATOR : NULL
REMARK 200 OPTICS : NULL
REMARK 200
REMARK 200 DETECTOR TYPE : CCD
REMARK 200 DETECTOR MANUFACTURER : RAYONIX MX-225
REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS
REMARK 200 DATA SCALING SOFTWARE : XSCALE
REMARK 200
REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 43994
REMARK 200 RESOLUTION RANGE HIGH (A) : 1.500
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 : 29.00
REMARK 200 R MERGE (I) : NULL
REMARK 200 R SYM (I) : NULL
REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 85.0000
REMARK 200
REMARK 200 IN THE HIGHEST RESOLUTION SHELL.
REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.50
REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.53
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 (%): 44.37
REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.21
REMARK 280
REMARK 280 CRYSTALLIZATION CONDITIONS: TRIS-HCL (PH 8.5), PEG 200, KCL,
REMARK 280 MGCL2, SODIUM CITRATE, VAPOR DIFFUSION, HANGING DROP,
REMARK 280 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 50.39850
REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 21.80450
REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 0.00000
REMARK 290 SMTRY1 4 -1.000000 0.000000 0.000000 50.39850
REMARK 290 SMTRY2 4 0.000000 1.000000 0.000000 21.80450
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: 6850 ANGSTROM**2
REMARK 350 SURFACE AREA OF THE COMPLEX: 22490 ANGSTROM**2
REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -73.0 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 64.92012
REMARK 350 BIOMT2 2 0.000000 1.000000 0.000000 0.00000
REMARK 350 BIOMT3 2 0.000000 0.000000 -1.000000 62.97547
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 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 ASP A 281 CG OD1 OD2
REMARK 470 GLU A 283 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 O HOH A 692 O HOH A 799 2.10
REMARK 500 O HOH A 731 O HOH A 764 2.13
REMARK 500 NH2 ARG A 356 O HOH A 601 2.14
REMARK 500 O HOH A 611 O HOH A 812 2.17
REMARK 500 O HOH A 626 O HOH A 857 2.18
REMARK 500 O HOH A 607 O HOH A 800 2.19
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 207 62.04 -104.90
REMARK 500 GLU A 238 -67.26 -127.68
REMARK 500 ASP A 292 -124.92 57.48
REMARK 500 ASP A 334 88.82 62.75
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 873 DISTANCE = 6.60 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 MG A 503 MG
REMARK 620 N RES CSSEQI ATOM
REMARK 620 1 GLU A 207 OE2
REMARK 620 2 GLU A 396 OE1 76.2
REMARK 620 3 ATP A 504 O1G 71.0 5.1
REMARK 620 4 ATP A 504 O1B 74.7 3.2 4.6
REMARK 620 5 HOH A 637 O 77.9 1.8 6.9 4.7
REMARK 620 6 HOH A 716 O 74.5 4.6 5.4 7.0 5.0
REMARK 620 N 1 2 3 4 5
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 89.7
REMARK 620 3 ATP A 504 O1B 90.5 172.7
REMARK 620 4 ATP A 504 O1A 94.5 95.0 92.3
REMARK 620 5 HOH A 637 O 87.2 89.3 83.4 175.4
REMARK 620 6 HOH A 732 O 173.4 90.4 88.6 92.1 86.2
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 O2G
REMARK 620 2 ATP A 504 O2B 89.2
REMARK 620 3 HOH A 640 O 94.1 91.4
REMARK 620 4 HOH A 682 O 176.5 87.4 85.1
REMARK 620 5 HOH A 691 O 94.5 176.2 88.1 88.9
REMARK 620 6 HOH A 750 O 90.5 90.5 175.0 90.4 89.8
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 9U6 A 505
REMARK 900
REMARK 900 RELATED ENTRIES
REMARK 900 RELATED ID: 6AAC RELATED DB: PDB
REMARK 900 RELATED ID: 6AAD RELATED DB: PDB
REMARK 900 RELATED ID: 6AAN RELATED DB: PDB
REMARK 900 RELATED ID: 6AAO RELATED DB: PDB
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 6AAP A 185 454 UNP Q8PWY1 PYLS_METMA 185 454
SEQADV 6AAP GLY A 181 UNP Q8PWY1 EXPRESSION TAG
SEQADV 6AAP SER A 182 UNP Q8PWY1 EXPRESSION TAG
SEQADV 6AAP HIS A 183 UNP Q8PWY1 EXPRESSION TAG
SEQADV 6AAP MET A 184 UNP Q8PWY1 EXPRESSION TAG
SEQADV 6AAP ALA A 306 UNP Q8PWY1 TYR 306 ENGINEERED MUTATION
SEQADV 6AAP PHE A 384 UNP Q8PWY1 TYR 384 ENGINEERED MUTATION
SEQADV 6AAP 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 9U6 A 505 40
HETNAM MG MAGNESIUM ION
HETNAM ATP ADENOSINE-5'-TRIPHOSPHATE
HETNAM 9U6 3-[(2-{[(BENZYLOXY)CARBONYL]AMINO}ETHYL)SELANYL]-L-
HETNAM 2 9U6 ALANINE
FORMUL 2 MG 3(MG 2+)
FORMUL 5 ATP C10 H16 N5 O13 P3
FORMUL 6 9U6 C13 H18 N2 O4 SE
FORMUL 7 HOH *273(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 THR A 282 GLN A 287 1 6
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 VAL A 390 O LEU A 397
SHEET 7 AA1 7 LYS A 375 CYS A 381 -1 N VAL A 377 O ASP A 389
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 OE2 GLU A 207 MG MG A 503 1555 4546 2.00
LINK OE2 GLU A 396 MG MG A 502 1555 1555 2.11
LINK OE1 GLU A 396 MG MG A 503 1555 1555 2.11
LINK OG SER A 399 MG MG A 502 1555 1555 2.06
LINK MG MG A 501 O2G ATP A 504 1555 1555 2.06
LINK MG MG A 501 O2B ATP A 504 1555 1555 2.01
LINK MG MG A 501 O HOH A 640 1555 1555 2.05
LINK MG MG A 501 O HOH A 682 1555 1555 2.19
LINK MG MG A 501 O HOH A 691 1555 1555 2.07
LINK MG MG A 501 O HOH A 750 1555 1555 2.12
LINK MG MG A 502 O1B ATP A 504 1555 1555 2.07
LINK MG MG A 502 O1A ATP A 504 1555 1555 2.03
LINK MG MG A 502 O HOH A 637 1555 1555 2.17
LINK MG MG A 502 O HOH A 732 1555 1555 2.07
LINK MG MG A 503 O1G ATP A 504 1555 1555 2.09
LINK MG MG A 503 O1B ATP A 504 1555 1555 2.24
LINK MG MG A 503 O HOH A 637 1555 1555 2.23
LINK MG MG A 503 O HOH A 716 1555 4556 2.09
CISPEP 1 ASP A 318 PRO A 319 0 -1.21
CISPEP 2 GLY A 403 PRO A 404 0 -2.03
SITE 1 AC1 5 ATP A 504 HOH A 640 HOH A 682 HOH A 691
SITE 2 AC1 5 HOH A 750
SITE 1 AC2 6 GLU A 396 SER A 399 MG A 503 ATP A 504
SITE 2 AC2 6 HOH A 637 HOH A 732
SITE 1 AC3 6 GLU A 207 GLU A 396 MG A 502 ATP A 504
SITE 2 AC3 6 HOH A 637 HOH A 716
SITE 1 AC4 31 GLU A 207 ARG A 330 GLU A 332 HIS A 338
SITE 2 AC4 31 LEU A 339 PHE A 342 MET A 344 GLU A 396
SITE 3 AC4 31 LEU A 397 SER A 398 SER A 399 GLY A 421
SITE 4 AC4 31 GLY A 423 ARG A 426 MG A 501 MG A 502
SITE 5 AC4 31 MG A 503 9U6 A 505 HOH A 611 HOH A 637
SITE 6 AC4 31 HOH A 640 HOH A 682 HOH A 691 HOH A 716
SITE 7 AC4 31 HOH A 731 HOH A 732 HOH A 745 HOH A 748
SITE 8 AC4 31 HOH A 750 HOH A 764 HOH A 768
SITE 1 AC5 17 MET A 276 MET A 300 ALA A 302 ALA A 306
SITE 2 AC5 17 LEU A 309 ARG A 330 ASN A 346 CYS A 348
SITE 3 AC5 17 PHE A 384 SER A 399 ASP A 408 ILE A 413
SITE 4 AC5 17 TRP A 417 GLY A 421 ATP A 504 HOH A 603
SITE 5 AC5 17 HOH A 787
CRYST1 100.797 43.609 72.478 90.00 119.67 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 0.009921 0.000000 0.005651 0.00000
SCALE2 0.000000 0.022931 0.000000 0.00000
SCALE3 0.000000 0.000000 0.015879 0.00000