2ZIN - Header Asymmetric Unit

HEADER LIGASE 19-FEB-08 2ZIN

TITLE CRYSTAL STRUCTURE OF THE CATALYTIC DOMAIN OF PYRROLYSYL- TITLE 2 TRNA SYNTHETASE IN COMPLEX WITH BOCLYS AND AN ATP ANALOGUE

COMPND MOL_ID: 1; COMPND 2 MOLECULE: PYRROLYSYL-TRNA SYNTHETASE; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: PYRROLYSINE--TRNA LIGASE, PYLRS; COMPND 5 EC: 6.1.1.26; COMPND 6 ENGINEERED: YES

SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: METHANOSARCINA MAZEI; SOURCE 3 ORGANISM_TAXID: 2209; SOURCE 4 STRAIN: JCM9314; SOURCE 5 GENE: PYLS; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 8 EXPRESSION_SYSTEM_STRAIN: BL21(DE3) CODON PLUS; SOURCE 9 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 10 EXPRESSION_SYSTEM_PLASMID: PET28C

KEYWDS AMINOACYL-TRNA SYNTHETASE, PYRROLYSYL-TRNA SYNTHETASE, KEYWDS 2 PYRROLYSINE, TRNA, ATP ANALOGUE, NON-NATURAL AMINO ACID, KEYWDS 3 UNNATURAL AMINO ACID, ATP-BINDING, CYTOPLASM, LIGASE, KEYWDS 4 NUCLEOTIDE-BINDING, PROTEIN BIOSYNTHESIS, STRUCTURAL KEYWDS 5 GENOMICS, NPPSFA, NATIONAL PROJECT ON PROTEIN STRUCTURAL KEYWDS 6 AND FUNCTIONAL ANALYSES, RIKEN STRUCTURAL KEYWDS 7 GENOMICS/PROTEOMICS INITIATIVE, RSGI

EXPDTA X-RAY DIFFRACTION

AUTHOR T.YANAGISAWA,R.ISHII,S.YOKOYAMA,RIKEN STRUCTURAL AUTHOR 2 GENOMICS/PROTEOMICS INITIATIVE (RSGI)

REVDAT 1 02-DEC-08 2ZIN 0

JRNL AUTH T.YANAGISAWA,R.ISHII,R.FUKUNAGA,T.KOBAYASHI, JRNL AUTH 2 K.SAKAMOTO,S.YOKOYAMA JRNL TITL MULTISTEP ENGINEERING OF PYRROLYSYL-TRNA JRNL TITL 2 SYNTHETASE TO GENETICALLY ENCODE JRNL TITL 3 N(VAREPSILON)-(O-AZIDOBENZYLOXYCARBONYL) LYSINE JRNL TITL 4 FOR SITE-SPECIFIC PROTEIN MODIFICATION JRNL REF CHEM.BIOL. V. 15 1187 2008 JRNL REFN ISSN 1074-5521 JRNL PMID 19022179 JRNL DOI 10.1016/J.CHEMBIOL.2008.10.004

REMARK 1

REMARK 2 REMARK 2 RESOLUTION. 1.79 ANGSTROMS.

REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : CNS 1.1 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 : NULL REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.79 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 34.28 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 DATA CUTOFF HIGH (ABS(F)) : 1595795.850 REMARK 3 DATA CUTOFF LOW (ABS(F)) : 0.0000 REMARK 3 COMPLETENESS (WORKING+TEST) (%) : 99.3 REMARK 3 NUMBER OF REFLECTIONS : 41325 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) : 0.190 REMARK 3 FREE R VALUE : 0.222 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 10.100 REMARK 3 FREE R VALUE TEST SET COUNT : 4162 REMARK 3 ESTIMATED ERROR OF FREE R VALUE : 0.003 REMARK 3 REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN. REMARK 3 TOTAL NUMBER OF BINS USED : 6 REMARK 3 BIN RESOLUTION RANGE HIGH (A) : 1.79 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.90 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 98.00 REMARK 3 REFLECTIONS IN BIN (WORKING SET) : 6058 REMARK 3 BIN R VALUE (WORKING SET) : 0.3550 REMARK 3 BIN FREE R VALUE : 0.3720 REMARK 3 BIN FREE R VALUE TEST SET SIZE (%) : 10.20 REMARK 3 BIN FREE R VALUE TEST SET COUNT : 690 REMARK 3 ESTIMATED ERROR OF BIN FREE R VALUE : 0.014 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 2095 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 54 REMARK 3 SOLVENT ATOMS : 217 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 29.60 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 46.10 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -3.80000 REMARK 3 B22 (A**2) : -3.80000 REMARK 3 B33 (A**2) : 7.59000 REMARK 3 B12 (A**2) : 1.13000 REMARK 3 B13 (A**2) : 0.00000 REMARK 3 B23 (A**2) : 0.00000 REMARK 3 REMARK 3 ESTIMATED COORDINATE ERROR. REMARK 3 ESD FROM LUZZATI PLOT (A) : 0.21 REMARK 3 ESD FROM SIGMAA (A) : 0.36 REMARK 3 LOW RESOLUTION CUTOFF (A) : 5.00 REMARK 3 REMARK 3 CROSS-VALIDATED ESTIMATED COORDINATE ERROR. REMARK 3 ESD FROM C-V LUZZATI PLOT (A) : 0.25 REMARK 3 ESD FROM C-V SIGMAA (A) : 0.39 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES. REMARK 3 BOND LENGTHS (A) : 0.010 REMARK 3 BOND ANGLES (DEGREES) : 1.60 REMARK 3 DIHEDRAL ANGLES (DEGREES) : 23.40 REMARK 3 IMPROPER ANGLES (DEGREES) : 1.86 REMARK 3 REMARK 3 ISOTROPIC THERMAL MODEL : RESTRAINED REMARK 3 REMARK 3 ISOTROPIC THERMAL FACTOR RESTRAINTS. RMS SIGMA REMARK 3 MAIN-CHAIN BOND (A**2) : 4.080 ; 1.500 REMARK 3 MAIN-CHAIN ANGLE (A**2) : 5.200 ; 2.000 REMARK 3 SIDE-CHAIN BOND (A**2) : 6.330 ; 2.000 REMARK 3 SIDE-CHAIN ANGLE (A**2) : 8.200 ; 2.500 REMARK 3 REMARK 3 BULK SOLVENT MODELING. REMARK 3 METHOD USED : FLAT MODEL REMARK 3 KSOL : 0.35 REMARK 3 BSOL : 69.04 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 : PROTEIN_REP.PARAM REMARK 3 PARAMETER FILE 2 : WATER_REP.PARAM REMARK 3 PARAMETER FILE 3 : ION.PARAM REMARK 3 PARAMETER FILE 4 : LIGAND2.PARAM REMARK 3 PARAMETER FILE 5 : NULL REMARK 3 TOPOLOGY FILE 1 : PROTEIN.TOP REMARK 3 TOPOLOGY FILE 2 : WATER.TOP REMARK 3 TOPOLOGY FILE 3 : ION.TOP REMARK 3 TOPOLOGY FILE 4 : LIGAND2.TOP REMARK 3 TOPOLOGY FILE 5 : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL

REMARK 4 REMARK 4 2ZIN COMPLIES WITH FORMAT V. 3.20, 01-DEC-08

REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 20-FEB-08. REMARK 100 THE RCSB ID CODE IS RCSB028019.

REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 15-DEC-04 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 7.0 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : SPRING-8 REMARK 200 BEAMLINE : BL41XU REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.0000 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 315 REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 41338 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.790 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 (%) : 99.3 REMARK 200 DATA REDUNDANCY : NULL REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : 0.06300 REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : NULL REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.79 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.82 REMARK 200 COMPLETENESS FOR SHELL (%) : 96.0 REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : 0.48600 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: MOLREP REMARK 200 STARTING MODEL: 1WK3 REMARK 200 REMARK 200 REMARK: NULL

REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 63.27 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 3.35 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: NA/CACODYLATE, MGCL2, PEG3350, PH REMARK 280 7.0, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 293K

REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 64 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -Y,X-Y,Z+1/3 REMARK 290 3555 -X+Y,-X,Z+2/3 REMARK 290 4555 -X,-Y,Z REMARK 290 5555 Y,-X+Y,Z+1/3 REMARK 290 6555 X-Y,X,Z+2/3 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 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 2 0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 23.51667 REMARK 290 SMTRY1 3 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 3 -0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 47.03333 REMARK 290 SMTRY1 4 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 5 0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 5 -0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 5 0.000000 0.000000 1.000000 23.51667 REMARK 290 SMTRY1 6 0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 6 0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 6 0.000000 0.000000 1.000000 47.03333 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: 7280 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 22940 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -49.0 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 -52.35500 REMARK 350 BIOMT2 2 0.000000 -1.000000 0.000000 90.68152 REMARK 350 BIOMT3 2 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 MET A -21 REMARK 465 GLY A -20 REMARK 465 SER A -19 REMARK 465 SER A -18 REMARK 465 HIS A -17 REMARK 465 HIS A -16 REMARK 465 HIS A -15 REMARK 465 HIS A -14 REMARK 465 HIS A -13 REMARK 465 HIS A -12 REMARK 465 SER A -11 REMARK 465 SER A -10 REMARK 465 GLY A -9 REMARK 465 LEU A -8 REMARK 465 VAL A -7 REMARK 465 PRO A -6 REMARK 465 ARG A -5 REMARK 465 GLY A -4 REMARK 465 SER A -3 REMARK 465 HIS A -2 REMARK 465 MET A -1 REMARK 465 ALA A 185 REMARK 465 SER A 186 REMARK 465 ALA A 187 REMARK 465 ILE A 208 REMARK 465 SER A 209 REMARK 465 LEU A 210 REMARK 465 ASN A 211 REMARK 465 SER A 380 REMARK 465 CYS A 381 REMARK 465 MET A 382 REMARK 465 VAL A 383 REMARK 465 TYR A 384

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 N ASP A 414 O HOH A 2071 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 ARG A 298 NE - CZ - NH1 ANGL. DEV. = 4.2 DEGREES REMARK 500 ARG A 298 NE - CZ - NH2 ANGL. DEV. = -3.9 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 GLU A 237 -90.97 -107.77 REMARK 500 ASN A 280 -0.68 -47.24 REMARK 500 ASP A 292 -157.70 59.13 REMARK 500 ILE A 413 -74.91 -85.06 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 A2074 DISTANCE = 6.83 ANGSTROMS REMARK 525 HOH A2123 DISTANCE = 7.45 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 702 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 SER A 399 OG REMARK 620 2 ANP A 501 O2B 173.2 REMARK 620 3 ANP A 501 O1A 93.7 80.0 REMARK 620 4 HOH A2060 O 100.3 84.5 154.0 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MG A 701 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HOH A2141 O REMARK 620 2 HOH A2188 O 91.8 REMARK 620 3 HOH A2161 O 85.1 93.9 REMARK 620 4 ANP A 501 O1G 94.7 173.0 89.4 REMARK 620 5 HOH A2193 O 94.0 93.8 172.3 83.0 REMARK 620 6 ANP A 501 O1B 171.3 86.5 86.5 87.5 94.6 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 701 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MG A 702 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ANP A 501 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE LBY A 601 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE EDO A 2011

REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 2E3C RELATED DB: PDB REMARK 900 THE LIGAND-FREE FORM REMARK 900 RELATED ID: 2ZCD RELATED DB: PDB REMARK 900 THE AMPPNP-BOUND FORM REMARK 900 RELATED ID: 2ZCE RELATED DB: PDB REMARK 900 THE PYRROLYSINE/AMPPNP-BOUND FORM REMARK 900 RELATED ID: TRT001000322.2 RELATED DB: TARGETDB

REMARK 999 REMARK 999 SEQUENCE REMARK 999 THIS CONFLICT IS DUE TO THE STRAIN DIFFERENCE REMARK 999 (JCM9314 AND GOE1).

DBREF 2ZIN A 185 454 UNP Q8PWY1 PYLS_METMA 185 454

SEQADV 2ZIN MET A -21 UNP Q8PWY1 EXPRESSION TAG SEQADV 2ZIN GLY A -20 UNP Q8PWY1 EXPRESSION TAG SEQADV 2ZIN SER A -19 UNP Q8PWY1 EXPRESSION TAG SEQADV 2ZIN SER A -18 UNP Q8PWY1 EXPRESSION TAG SEQADV 2ZIN HIS A -17 UNP Q8PWY1 EXPRESSION TAG SEQADV 2ZIN HIS A -16 UNP Q8PWY1 EXPRESSION TAG SEQADV 2ZIN HIS A -15 UNP Q8PWY1 EXPRESSION TAG SEQADV 2ZIN HIS A -14 UNP Q8PWY1 EXPRESSION TAG SEQADV 2ZIN HIS A -13 UNP Q8PWY1 EXPRESSION TAG SEQADV 2ZIN HIS A -12 UNP Q8PWY1 EXPRESSION TAG SEQADV 2ZIN SER A -11 UNP Q8PWY1 EXPRESSION TAG SEQADV 2ZIN SER A -10 UNP Q8PWY1 EXPRESSION TAG SEQADV 2ZIN GLY A -9 UNP Q8PWY1 EXPRESSION TAG SEQADV 2ZIN LEU A -8 UNP Q8PWY1 EXPRESSION TAG SEQADV 2ZIN VAL A -7 UNP Q8PWY1 EXPRESSION TAG SEQADV 2ZIN PRO A -6 UNP Q8PWY1 EXPRESSION TAG SEQADV 2ZIN ARG A -5 UNP Q8PWY1 EXPRESSION TAG SEQADV 2ZIN GLY A -4 UNP Q8PWY1 EXPRESSION TAG SEQADV 2ZIN SER A -3 UNP Q8PWY1 EXPRESSION TAG SEQADV 2ZIN HIS A -2 UNP Q8PWY1 EXPRESSION TAG SEQADV 2ZIN MET A -1 UNP Q8PWY1 EXPRESSION TAG SEQADV 2ZIN GLY A 444 UNP Q8PWY1 GLU 444 SEE REMARK 999

SEQRES 1 A 291 MET GLY SER SER HIS HIS HIS HIS HIS HIS SER SER GLY SEQRES 2 A 291 LEU VAL PRO ARG GLY SER HIS MET ALA SER ALA PRO ALA SEQRES 3 A 291 LEU THR LYS SER GLN THR ASP ARG LEU GLU VAL LEU LEU SEQRES 4 A 291 ASN PRO LYS ASP GLU ILE SER LEU ASN SER GLY LYS PRO SEQRES 5 A 291 PHE ARG GLU LEU GLU SER GLU LEU LEU SER ARG ARG LYS SEQRES 6 A 291 LYS ASP LEU GLN GLN ILE TYR ALA GLU GLU ARG GLU ASN SEQRES 7 A 291 TYR LEU GLY LYS LEU GLU ARG GLU ILE THR ARG PHE PHE SEQRES 8 A 291 VAL ASP ARG GLY PHE LEU GLU ILE LYS SER PRO ILE LEU SEQRES 9 A 291 ILE PRO LEU GLU TYR ILE GLU ARG MET GLY ILE ASP ASN SEQRES 10 A 291 ASP THR GLU LEU SER LYS GLN ILE PHE ARG VAL ASP LYS SEQRES 11 A 291 ASN PHE CYS LEU ARG PRO MET LEU ALA PRO ASN LEU TYR SEQRES 12 A 291 ASN TYR LEU ARG LYS LEU ASP ARG ALA LEU PRO ASP PRO SEQRES 13 A 291 ILE LYS ILE PHE GLU ILE GLY PRO CYS TYR ARG LYS GLU SEQRES 14 A 291 SER ASP GLY LYS GLU HIS LEU GLU GLU PHE THR MET LEU SEQRES 15 A 291 ASN PHE CYS GLN MET GLY SER GLY CYS THR ARG GLU ASN SEQRES 16 A 291 LEU GLU SER ILE ILE THR ASP PHE LEU ASN HIS LEU GLY SEQRES 17 A 291 ILE ASP PHE LYS ILE VAL GLY ASP SER CYS MET VAL TYR SEQRES 18 A 291 GLY ASP THR LEU ASP VAL MET HIS GLY ASP LEU GLU LEU SEQRES 19 A 291 SER SER ALA VAL VAL GLY PRO ILE PRO LEU ASP ARG GLU SEQRES 20 A 291 TRP GLY ILE ASP LYS PRO TRP ILE GLY ALA GLY PHE GLY SEQRES 21 A 291 LEU GLU ARG LEU LEU LYS VAL LYS HIS ASP PHE LYS ASN SEQRES 22 A 291 ILE LYS ARG ALA ALA ARG SER GLY SER TYR TYR ASN GLY SEQRES 23 A 291 ILE SER THR ASN LEU

HET MG A 701 1 HET MG A 702 1 HET ANP A 501 31 HET LBY A 601 17 HET EDO A2011 4

HETNAM MG MAGNESIUM ION HETNAM ANP PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER HETNAM LBY N~6~-(TERT-BUTOXYCARBONYL)-L-LYSINE HETNAM EDO 1,2-ETHANEDIOL

HETSYN EDO ETHYLENE GLYCOL

FORMUL 2 MG 2(MG 2+) FORMUL 4 ANP C10 H17 N6 O12 P3 FORMUL 5 LBY C11 H22 N2 O4 FORMUL 6 EDO C2 H6 O2 FORMUL 7 HOH *217(H2 O)

HELIX 1 1 THR A 191 LEU A 202 1 12 HELIX 2 2 PRO A 215 GLU A 237 1 23 HELIX 3 3 ASN A 241 ARG A 257 1 17 HELIX 4 4 LEU A 270 MET A 276 1 7 HELIX 5 5 GLU A 283 ILE A 288 5 6 HELIX 6 6 LEU A 301 ASP A 313 1 13 HELIX 7 7 THR A 355 GLY A 371 1 17 HELIX 8 8 ILE A 405 GLY A 412 5 8 HELIX 9 9 LEU A 424 HIS A 432 1 9 HELIX 10 10 ASN A 436 ALA A 441 5 6

SHEET 1 A 7 LEU A 260 ILE A 262 0 SHEET 2 A 7 ILE A 320 TYR A 329 1 O LYS A 321 N LEU A 260 SHEET 3 A 7 GLU A 341 MET A 350 -1 O MET A 344 N GLY A 326 SHEET 4 A 7 TRP A 417 GLY A 423 -1 O PHE A 422 N LEU A 345 SHEET 5 A 7 LEU A 395 VAL A 402 -1 N SER A 399 O GLY A 421 SHEET 6 A 7 ASP A 386 HIS A 392 -1 N LEU A 388 O ALA A 400 SHEET 7 A 7 LYS A 375 VAL A 377 -1 N VAL A 377 O ASP A 389 SHEET 1 B 3 LEU A 267 PRO A 269 0 SHEET 2 B 3 PHE A 295 LEU A 297 -1 O CYS A 296 N ILE A 268 SHEET 3 B 3 ARG A 290 VAL A 291 -1 N VAL A 291 O PHE A 295 SHEET 1 C 2 TYR A 446 TYR A 447 0 SHEET 2 C 2 ILE A 450 SER A 451 -1 O ILE A 450 N TYR A 447

LINK OG SER A 399 MG MG A 702 1555 1555 2.26 LINK MG MG A 701 O HOH A2141 1555 1555 2.28 LINK MG MG A 701 O HOH A2188 1555 1555 2.27 LINK MG MG A 701 O HOH A2161 1555 1555 2.22 LINK MG MG A 701 O1G ANP A 501 1555 1555 2.10 LINK MG MG A 701 O HOH A2193 1555 1555 2.35 LINK MG MG A 701 O1B ANP A 501 1555 1555 2.19 LINK MG MG A 702 O2B ANP A 501 1555 1555 2.25 LINK MG MG A 702 O1A ANP A 501 1555 1555 2.44 LINK MG MG A 702 O HOH A2060 1555 1555 2.33

CISPEP 1 ASP A 318 PRO A 319 0 -0.12 CISPEP 2 GLY A 403 PRO A 404 0 0.19

SITE 1 AC1 4 HOH A2141 HOH A2161 HOH A2188 HOH A2193 SITE 1 AC2 3 GLU A 396 SER A 399 HOH A2060 SITE 1 AC3 20 ARG A 330 GLU A 332 HIS A 338 LEU A 339 SITE 2 AC3 20 PHE A 342 GLU A 396 LEU A 397 SER A 398 SITE 3 AC3 20 SER A 399 GLY A 421 GLY A 423 ARG A 426 SITE 4 AC3 20 HOH A2013 HOH A2053 HOH A2057 HOH A2060 SITE 5 AC3 20 HOH A2076 HOH A2161 HOH A2188 HOH A2193 SITE 1 AC4 8 MET A 300 TYR A 306 ASN A 346 CYS A 348 SITE 2 AC4 8 TRP A 417 GLY A 419 ALA A 420 HOH A2012 SITE 1 AC5 3 MET A 276 TRP A 417 HOH A2221

CRYST1 104.710 104.710 70.550 90.00 90.00 120.00 P 64 6

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 0.009550 0.005514 0.000000 0.00000

SCALE2 0.000000 0.011028 0.000000 0.00000

SCALE3 0.000000 0.000000 0.014174 0.00000