PDB Short entry for 2D1R HEADER OXIDOREDUCTASE 31-AUG-05 2D1R TITLE CRYSTAL STRUCTURE OF THE THERMOSTABLE JAPANESE FIREFLY LUCIFERASE TITLE 2 COMPLEXED WITH OXYLUCIFERIN AND AMP COMPND MOL_ID: 1; COMPND 2 MOLECULE: LUCIFERIN 4-MONOOXYGENASE; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: LUCIFERASE; COMPND 5 EC: 1.13.12.7; COMPND 6 ENGINEERED: YES; COMPND 7 MUTATION: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: LUCIOLA CRUCIATA; SOURCE 3 ORGANISM_COMMON: JAPANESE FIREFLY; SOURCE 4 ORGANISM_TAXID: 7051; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 6 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 7 EXPRESSION_SYSTEM_STRAIN: HB101; SOURCE 8 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 9 EXPRESSION_SYSTEM_PLASMID: PUC18 KEYWDS ALPHA/BETA, BETA BARREL, ALPHA+BETA, RIKEN STRUCTURAL KEYWDS 2 GENOMICS/PROTEOMICS INITIATIVE, RSGI, STRUCTURAL GENOMICS, KEYWDS 3 OXIDOREDUCTASE EXPDTA X-RAY DIFFRACTION AUTHOR T.NAKATSU,S.ICHIYAMA,J.HIRATAKE,A.SALDANHA,N.KOBASHI,K.SAKATA,H.KATO, AUTHOR 2 RIKEN STRUCTURAL GENOMICS/PROTEOMICS INITIATIVE (RSGI) REVDAT 5 15-NOV-23 2D1R 1 REMARK REVDAT 4 25-OCT-23 2D1R 1 REMARK REVDAT 3 10-NOV-21 2D1R 1 REMARK SEQADV LINK REVDAT 2 24-FEB-09 2D1R 1 VERSN REVDAT 1 21-MAR-06 2D1R 0 JRNL AUTH T.NAKATSU,S.ICHIYAMA,J.HIRATAKE,A.SALDANHA,N.KOBASHI, JRNL AUTH 2 K.SAKATA,H.KATO JRNL TITL STRUCTURAL BASIS FOR THE SPECTRAL DIFFERENCE IN LUCIFERASE JRNL TITL 2 BIOLUMINESCENCE. JRNL REF NATURE V. 440 372 2006 JRNL REFN ISSN 0028-0836 JRNL PMID 16541080 JRNL DOI 10.1038/NATURE04542 REMARK 2 REMARK 2 RESOLUTION. 1.60 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.1.24 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) : 1.60 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 55.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : NULL REMARK 3 NUMBER OF REFLECTIONS : 69987 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) : 0.185 REMARK 3 R VALUE (WORKING SET) : 0.184 REMARK 3 FREE R VALUE : 0.210 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.000 REMARK 3 FREE R VALUE TEST SET COUNT : 3718 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) : 1.60 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.64 REMARK 3 REFLECTION IN BIN (WORKING SET) : 4927 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : NULL REMARK 3 BIN R VALUE (WORKING SET) : 0.2550 REMARK 3 BIN FREE R VALUE SET COUNT : 276 REMARK 3 BIN FREE R VALUE : 0.2780 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 4103 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 39 REMARK 3 SOLVENT ATOMS : 626 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 16.44 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -0.16000 REMARK 3 B22 (A**2) : -0.27000 REMARK 3 B33 (A**2) : 0.43000 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): 0.092 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.090 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.052 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 1.469 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.954 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.941 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 4237 ; 0.011 ; 0.022 REMARK 3 BOND LENGTHS OTHERS (A): NULL ; NULL ; NULL REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 5752 ; 1.333 ; 1.985 REMARK 3 BOND ANGLES OTHERS (DEGREES): NULL ; NULL ; NULL REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 538 ; 5.559 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): NULL ; NULL ; NULL REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): NULL ; NULL ; NULL REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): NULL ; NULL ; NULL REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 664 ; 0.088 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 3142 ; 0.005 ; 0.020 REMARK 3 GENERAL PLANES OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): 1945 ; 0.196 ; 0.200 REMARK 3 NON-BONDED CONTACTS OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION OTHERS (A): NULL ; NULL ; NULL REMARK 3 H-BOND (X...Y) REFINED ATOMS (A): 465 ; 0.107 ; 0.200 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): 41 ; 0.188 ; 0.200 REMARK 3 SYMMETRY VDW OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY H-BOND REFINED ATOMS (A): 35 ; 0.102 ; 0.200 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): 2672 ; 0.726 ; 1.500 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 4336 ; 1.351 ; 2.000 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 1564 ; 2.111 ; 3.000 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 1416 ; 3.527 ; 4.500 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 : BABINET MODEL WITH 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: NULL REMARK 4 REMARK 4 2D1R COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 06-SEP-05. REMARK 100 THE DEPOSITION ID IS D_1000024880. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 29-MAR-01 REMARK 200 TEMPERATURE (KELVIN) : 90 REMARK 200 PH : 8.0 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : SPRING-8 REMARK 200 BEAMLINE : BL45XU REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.02 REMARK 200 MONOCHROMATOR : DIAMOND REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : RIGAKU JUPITER 210 REMARK 200 INTENSITY-INTEGRATION SOFTWARE : CRYSTALCLEAR (MSC/RIGAKU) REMARK 200 DATA SCALING SOFTWARE : CRYSTALCLEAR (MSC/RIGAKU) REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 73719 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.600 REMARK 200 RESOLUTION RANGE LOW (A) : 55.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 1.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.7 REMARK 200 DATA REDUNDANCY : 6.600 REMARK 200 R MERGE (I) : 0.05400 REMARK 200 R SYM (I) : NULL REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 10.1000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.60 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.66 REMARK 200 COMPLETENESS FOR SHELL (%) : 97.4 REMARK 200 DATA REDUNDANCY IN SHELL : 3.60 REMARK 200 R MERGE FOR SHELL (I) : 0.21000 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 <I/SIGMA(I)> FOR SHELL : 3.000 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: FOURIER SYNTHESIS REMARK 200 SOFTWARE USED: NULL REMARK 200 STARTING MODEL: PDB ENTRY 2D1Q 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): 2.30 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: PEG4000, LITHIUM CHROLIDE, MAGNESIUM REMARK 280 CHLORIDE, ATP, D-LUCIFERIN, TEIS-HCL, PH 8.0, VAPOR DIFFUSION, REMARK 280 TEMPERATURE 293K 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 28.80600 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 26.37150 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 90.70100 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 26.37150 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 28.80600 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 90.70100 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: MONOMERIC 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 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 1 REMARK 465 GLU A 2 REMARK 465 ASN A 3 REMARK 465 MET A 4 REMARK 465 GLU A 5 REMARK 465 ASN A 6 REMARK 465 ALA A 546 REMARK 465 LYS A 547 REMARK 465 MET A 548 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 LYS A 15 CD CE NZ REMARK 470 GLU A 22 CD OE1 OE2 REMARK 470 ARG A 30 NH1 NH2 REMARK 470 LYS A 184 NZ REMARK 470 LYS A 283 NZ REMARK 470 LEU A 293 CD1 CD2 REMARK 470 LYS A 305 CD CE NZ REMARK 470 LYS A 382 CD CE NZ REMARK 470 GLU A 408 CD OE1 OE2 REMARK 470 LYS A 411 CD CE NZ REMARK 470 GLU A 412 CD OE1 OE2 REMARK 470 LEU A 440 CD1 CD2 REMARK 470 LYS A 441 CD CE NZ REMARK 470 LYS A 445 CE NZ REMARK 470 SER A 491 OG REMARK 470 LYS A 493 NZ REMARK 470 GLU A 539 CG CD OE1 OE2 REMARK 470 LYS A 542 CD CE NZ REMARK 470 LYS A 543 CG CD CE NZ REMARK 470 VAL A 545 CG1 CG2 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 159 CB - CG - OD2 ANGL. DEV. = 5.5 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 THR A 348 -67.67 72.33 REMARK 500 SER A 349 -159.99 -142.28 REMARK 500 ASP A 358 41.24 -151.07 REMARK 500 LEU A 370 -2.34 78.56 REMARK 500 ASN A 406 65.70 -151.78 REMARK 500 LYS A 447 -128.68 49.64 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 AMP A 1001 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE OLU A 2001 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 2D1S RELATED DB: PDB REMARK 900 T217I MUTANT WITH SLU REMARK 900 RELATED ID: 2D1T RELATED DB: PDB REMARK 900 T217I AND S286N MUTANTS WITH CL AND SLU REMARK 900 RELATED ID: MY_001000084.2 RELATED DB: TARGETDB DBREF 2D1R A 1 548 UNP P13129 LUCI_LUCCR 1 548 SEQADV 2D1R CSO A 63 UNP P13129 CYS 63 MODIFIED RESIDUE SEQADV 2D1R CSO A 64 UNP P13129 CYS 64 MODIFIED RESIDUE SEQADV 2D1R ILE A 217 UNP P13129 THR 217 ENGINEERED MUTATION SEQRES 1 A 548 MET GLU ASN MET GLU ASN ASP GLU ASN ILE VAL VAL GLY SEQRES 2 A 548 PRO LYS PRO PHE TYR PRO ILE GLU GLU GLY SER ALA GLY SEQRES 3 A 548 THR GLN LEU ARG LYS TYR MET GLU ARG TYR ALA LYS LEU SEQRES 4 A 548 GLY ALA ILE ALA PHE THR ASN ALA VAL THR GLY VAL ASP SEQRES 5 A 548 TYR SER TYR ALA GLU TYR LEU GLU LYS SER CSO CSO LEU SEQRES 6 A 548 GLY LYS ALA LEU GLN ASN TYR GLY LEU VAL VAL ASP GLY SEQRES 7 A 548 ARG ILE ALA LEU CYS SER GLU ASN CYS GLU GLU PHE PHE SEQRES 8 A 548 ILE PRO VAL ILE ALA GLY LEU PHE ILE GLY VAL GLY VAL SEQRES 9 A 548 ALA PRO THR ASN GLU ILE TYR THR LEU ARG GLU LEU VAL SEQRES 10 A 548 HIS SER LEU GLY ILE SER LYS PRO THR ILE VAL PHE SER SEQRES 11 A 548 SER LYS LYS GLY LEU ASP LYS VAL ILE THR VAL GLN LYS SEQRES 12 A 548 THR VAL THR THR ILE LYS THR ILE VAL ILE LEU ASP SER SEQRES 13 A 548 LYS VAL ASP TYR ARG GLY TYR GLN CYS LEU ASP THR PHE SEQRES 14 A 548 ILE LYS ARG ASN THR PRO PRO GLY PHE GLN ALA SER SER SEQRES 15 A 548 PHE LYS THR VAL GLU VAL ASP ARG LYS GLU GLN VAL ALA SEQRES 16 A 548 LEU ILE MET ASN SER SER GLY SER THR GLY LEU PRO LYS SEQRES 17 A 548 GLY VAL GLN LEU THR HIS GLU ASN ILE VAL THR ARG PHE SEQRES 18 A 548 SER HIS ALA ARG ASP PRO ILE TYR GLY ASN GLN VAL SER SEQRES 19 A 548 PRO GLY THR ALA VAL LEU THR VAL VAL PRO PHE HIS HIS SEQRES 20 A 548 GLY PHE GLY MET PHE THR THR LEU GLY TYR LEU ILE CYS SEQRES 21 A 548 GLY PHE ARG VAL VAL MET LEU THR LYS PHE ASP GLU GLU SEQRES 22 A 548 THR PHE LEU LYS THR LEU GLN ASP TYR LYS CYS THR SER SEQRES 23 A 548 VAL ILE LEU VAL PRO THR LEU PHE ALA ILE LEU ASN LYS SEQRES 24 A 548 SER GLU LEU LEU ASN LYS TYR ASP LEU SER ASN LEU VAL SEQRES 25 A 548 GLU ILE ALA SER GLY GLY ALA PRO LEU SER LYS GLU VAL SEQRES 26 A 548 GLY GLU ALA VAL ALA ARG ARG PHE ASN LEU PRO GLY VAL SEQRES 27 A 548 ARG GLN GLY TYR GLY LEU THR GLU THR THR SER ALA ILE SEQRES 28 A 548 ILE ILE THR PRO GLU GLY ASP ASP LYS PRO GLY ALA SER SEQRES 29 A 548 GLY LYS VAL VAL PRO LEU PHE LYS ALA LYS VAL ILE ASP SEQRES 30 A 548 LEU ASP THR LYS LYS SER LEU GLY PRO ASN ARG ARG GLY SEQRES 31 A 548 GLU VAL CYS VAL LYS GLY PRO MET LEU MET LYS GLY TYR SEQRES 32 A 548 VAL ASN ASN PRO GLU ALA THR LYS GLU LEU ILE ASP GLU SEQRES 33 A 548 GLU GLY TRP LEU HIS THR GLY ASP ILE GLY TYR TYR ASP SEQRES 34 A 548 GLU GLU LYS HIS PHE PHE ILE VAL ASP ARG LEU LYS SER SEQRES 35 A 548 LEU ILE LYS TYR LYS GLY TYR GLN VAL PRO PRO ALA GLU SEQRES 36 A 548 LEU GLU SER VAL LEU LEU GLN HIS PRO SER ILE PHE ASP SEQRES 37 A 548 ALA GLY VAL ALA GLY VAL PRO ASP PRO VAL ALA GLY GLU SEQRES 38 A 548 LEU PRO GLY ALA VAL VAL VAL LEU GLU SER GLY LYS ASN SEQRES 39 A 548 MET THR GLU LYS GLU VAL MET ASP TYR VAL ALA SER GLN SEQRES 40 A 548 VAL SER ASN ALA LYS ARG LEU ARG GLY GLY VAL ARG PHE SEQRES 41 A 548 VAL ASP GLU VAL PRO LYS GLY LEU THR GLY LYS ILE ASP SEQRES 42 A 548 GLY ARG ALA ILE ARG GLU ILE LEU LYS LYS PRO VAL ALA SEQRES 43 A 548 LYS MET MODRES 2D1R CSO A 63 CYS S-HYDROXYCYSTEINE MODRES 2D1R CSO A 64 CYS S-HYDROXYCYSTEINE HET CSO A 63 7 HET CSO A 64 7 HET AMP A1001 23 HET OLU A2001 16 HETNAM CSO S-HYDROXYCYSTEINE HETNAM AMP ADENOSINE MONOPHOSPHATE HETNAM OLU 2-(6-HYDROXY-1,3-BENZOTHIAZOL-2-YL)-1,3-THIAZOL-4(5H)- HETNAM 2 OLU ONE HETSYN OLU OXYLUCIFERIN FORMUL 1 CSO 2(C3 H7 N O3 S) FORMUL 2 AMP C10 H14 N5 O7 P FORMUL 3 OLU C10 H6 N2 O2 S2 FORMUL 4 HOH *626(H2 O) HELIX 1 1 SER A 24 GLY A 40 1 17 HELIX 2 2 TYR A 55 GLY A 73 1 19 HELIX 3 3 PHE A 90 GLY A 101 1 12 HELIX 4 4 THR A 112 LYS A 124 1 13 HELIX 5 5 GLY A 134 VAL A 145 1 12 HELIX 6 6 CYS A 165 ASN A 173 1 9 HELIX 7 7 GLN A 179 PHE A 183 5 5 HELIX 8 8 HIS A 214 ARG A 225 1 12 HELIX 9 9 HIS A 247 CYS A 260 1 14 HELIX 10 10 ASP A 271 TYR A 282 1 12 HELIX 11 11 VAL A 290 THR A 292 5 3 HELIX 12 12 LEU A 293 SER A 300 1 8 HELIX 13 13 LEU A 302 TYR A 306 5 5 HELIX 14 14 SER A 322 PHE A 333 1 12 HELIX 15 15 THR A 345 THR A 348 5 4 HELIX 16 16 ASN A 406 ILE A 414 1 9 HELIX 17 17 LYS A 441 LEU A 443 5 3 HELIX 18 18 PRO A 452 GLN A 462 1 11 HELIX 19 19 THR A 496 VAL A 508 1 13 HELIX 20 20 SER A 509 ARG A 513 5 5 HELIX 21 21 ASP A 533 LYS A 543 1 11 SHEET 1 A 5 VAL A 11 VAL A 12 0 SHEET 2 A 5 LYS A 372 ILE A 376 -1 O ALA A 373 N VAL A 11 SHEET 3 A 5 GLY A 390 LYS A 395 -1 O CYS A 393 N LYS A 374 SHEET 4 A 5 LEU A 420 TYR A 428 -1 O LEU A 420 N VAL A 394 SHEET 5 A 5 PHE A 434 ARG A 439 -1 O PHE A 435 N TYR A 427 SHEET 1 B 9 ASP A 52 SER A 54 0 SHEET 2 B 9 ILE A 42 ASN A 46 -1 N PHE A 44 O TYR A 53 SHEET 3 B 9 ARG A 263 MET A 266 1 O MET A 266 N THR A 45 SHEET 4 B 9 ALA A 238 THR A 241 1 N VAL A 239 O VAL A 265 SHEET 5 B 9 CYS A 284 LEU A 289 1 O THR A 285 N ALA A 238 SHEET 6 B 9 GLU A 313 SER A 316 1 O ALA A 315 N VAL A 287 SHEET 7 B 9 ARG A 339 GLY A 343 1 O ARG A 339 N ILE A 314 SHEET 8 B 9 ALA A 350 ILE A 353 -1 O ILE A 352 N TYR A 342 SHEET 9 B 9 LYS A 366 VAL A 367 -1 O LYS A 366 N ILE A 353 SHEET 1 C 4 GLY A 103 THR A 107 0 SHEET 2 C 4 ARG A 79 CYS A 83 1 N ILE A 80 O ALA A 105 SHEET 3 C 4 ILE A 127 SER A 130 1 O PHE A 129 N ALA A 81 SHEET 4 C 4 THR A 150 ILE A 153 1 O VAL A 152 N VAL A 128 SHEET 1 D 3 VAL A 194 MET A 198 0 SHEET 2 D 3 VAL A 210 THR A 213 -1 O LEU A 212 N ALA A 195 SHEET 3 D 3 GLY A 402 TYR A 403 -1 O GLY A 402 N GLN A 211 SHEET 1 E 3 ILE A 466 ASP A 476 0 SHEET 2 E 3 GLY A 480 LEU A 489 -1 O GLY A 484 N ALA A 472 SHEET 3 E 3 VAL A 518 PHE A 520 1 O ARG A 519 N VAL A 487 LINK C SER A 62 N CSO A 63 1555 1555 1.34 LINK C CSO A 63 N CSO A 64 1555 1555 1.34 LINK C CSO A 64 N LEU A 65 1555 1555 1.34 SITE 1 AC1 19 SER A 200 SER A 201 HIS A 247 GLY A 318 SITE 2 AC1 19 ALA A 319 PRO A 320 GLN A 340 GLY A 341 SITE 3 AC1 19 TYR A 342 GLY A 343 LEU A 344 THR A 345 SITE 4 AC1 19 ASP A 424 ARG A 439 LYS A 531 OLU A2001 SITE 5 AC1 19 HOH A2095 HOH A2229 HOH A2337 SITE 1 AC2 12 HIS A 247 PHE A 249 THR A 253 GLY A 318 SITE 2 AC2 12 GLY A 341 GLY A 343 LEU A 344 THR A 345 SITE 3 AC2 12 ALA A 350 AMP A1001 HOH A2002 HOH A2325 CRYST1 57.612 181.402 52.743 90.00 90.00 90.00 P 21 21 21 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 0.017357 0.000000 0.000000 0.00000 SCALE2 0.000000 0.005513 0.000000 0.00000 SCALE3 0.000000 0.000000 0.018960 0.00000