HEADER TRANSFERASE 23-MAY-16 5K5B
TITLE WILD-TYPE PAS-GAF FRAGMENT FROM DEINOCOCCUS RADIODURANS BPHP
COMPND MOL_ID: 1;
COMPND 2 MOLECULE: BACTERIOPHYTOCHROME;
COMPND 3 CHAIN: A;
COMPND 4 SYNONYM: PHYTOCHROME-LIKE PROTEIN;
COMPND 5 EC: 2.7.13.3;
COMPND 6 ENGINEERED: YES
SOURCE MOL_ID: 1;
SOURCE 2 ORGANISM_SCIENTIFIC: DEINOCOCCUS RADIODURANS;
SOURCE 3 ORGANISM_TAXID: 243230;
SOURCE 4 STRAIN: ATCC 13939 / DSM 20539 / JCM 16871 / LMG 4051 / NBRC 15346 /
SOURCE 5 NCIMB 9279 / R1 / VKM B-1422;
SOURCE 6 ATCC: 13939;
SOURCE 7 GENE: BPHP, DR_A0050;
SOURCE 8 EXPRESSION_SYSTEM: ESCHERICHIA COLI;
SOURCE 9 EXPRESSION_SYSTEM_TAXID: 469008;
SOURCE 10 EXPRESSION_SYSTEM_STRAIN: BL21(DE3);
SOURCE 11 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID;
SOURCE 12 EXPRESSION_SYSTEM_PLASMID: PET21B
KEYWDS KINASE PHOTOSENSOR TRANSFERASE PHYTOCHROME, TRANSFERASE
EXPDTA X-RAY DIFFRACTION
AUTHOR H.TAKALA,P.EDLUND,E.CLAESSON,J.A.IHALAINEN,S.WESTENHOFF
REVDAT 3 10-JAN-24 5K5B 1 COMPND HETNAM
REVDAT 2 02-NOV-16 5K5B 1 JRNL
REVDAT 1 26-OCT-16 5K5B 0
JRNL AUTH P.EDLUND,H.TAKALA,E.CLAESSON,L.HENRY,R.DODS,H.LEHTIVUORI,
JRNL AUTH 2 M.PANMAN,K.PANDE,T.WHITE,T.NAKANE,O.BERNTSSON,E.GUSTAVSSON,
JRNL AUTH 3 P.BATH,V.MODI,S.ROY-CHOWDHURY,J.ZOOK,P.BERNTSEN,S.PANDEY,
JRNL AUTH 4 I.POUDYAL,J.TENBOER,C.KUPITZ,A.BARTY,P.FROMME,J.D.KORALEK,
JRNL AUTH 5 T.TANAKA,J.SPENCE,M.LIANG,M.S.HUNTER,S.BOUTET,E.NANGO,
JRNL AUTH 6 K.MOFFAT,G.GROENHOF,J.IHALAINEN,E.A.STOJKOVIC,M.SCHMIDT,
JRNL AUTH 7 S.WESTENHOFF
JRNL TITL THE ROOM TEMPERATURE CRYSTAL STRUCTURE OF A BACTERIAL
JRNL TITL 2 PHYTOCHROME DETERMINED BY SERIAL FEMTOSECOND
JRNL TITL 3 CRYSTALLOGRAPHY.
JRNL REF SCI REP V. 6 35279 2016
JRNL REFN ESSN 2045-2322
JRNL PMID 27756898
JRNL DOI 10.1038/SREP35279
REMARK 2
REMARK 2 RESOLUTION. 1.35 ANGSTROMS.
REMARK 3
REMARK 3 REFINEMENT.
REMARK 3 PROGRAM : REFMAC 5.8.0135
REMARK 3 AUTHORS : MURSHUDOV,SKUBAK,LEBEDEV,PANNU,STEINER,
REMARK 3 : NICHOLLS,WINN,LONG,VAGIN
REMARK 3
REMARK 3 REFINEMENT TARGET : NULL
REMARK 3
REMARK 3 DATA USED IN REFINEMENT.
REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.35
REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 39.37
REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000
REMARK 3 COMPLETENESS FOR RANGE (%) : 98.1
REMARK 3 NUMBER OF REFLECTIONS : 72086
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) : 0.142
REMARK 3 R VALUE (WORKING SET) : 0.141
REMARK 3 FREE R VALUE : 0.171
REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.000
REMARK 3 FREE R VALUE TEST SET COUNT : 3795
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) : 1.35
REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.39
REMARK 3 REFLECTION IN BIN (WORKING SET) : 5211
REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 95.69
REMARK 3 BIN R VALUE (WORKING SET) : 0.2600
REMARK 3 BIN FREE R VALUE SET COUNT : 275
REMARK 3 BIN FREE R VALUE : 0.2880
REMARK 3
REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT.
REMARK 3 PROTEIN ATOMS : 2335
REMARK 3 NUCLEIC ACID ATOMS : 0
REMARK 3 HETEROGEN ATOMS : 63
REMARK 3 SOLVENT ATOMS : 322
REMARK 3
REMARK 3 B VALUES.
REMARK 3 FROM WILSON PLOT (A**2) : 25.09
REMARK 3 MEAN B VALUE (OVERALL, A**2) : 25.47
REMARK 3 OVERALL ANISOTROPIC B VALUE.
REMARK 3 B11 (A**2) : 0.08000
REMARK 3 B22 (A**2) : 0.00000
REMARK 3 B33 (A**2) : -0.07000
REMARK 3 B12 (A**2) : 0.00000
REMARK 3 B13 (A**2) : -0.20000
REMARK 3 B23 (A**2) : 0.00000
REMARK 3
REMARK 3 ESTIMATED OVERALL COORDINATE ERROR.
REMARK 3 ESU BASED ON R VALUE (A): 0.048
REMARK 3 ESU BASED ON FREE R VALUE (A): 0.047
REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.027
REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 1.483
REMARK 3
REMARK 3 CORRELATION COEFFICIENTS.
REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.977
REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.970
REMARK 3
REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT
REMARK 3 BOND LENGTHS REFINED ATOMS (A): 2576 ; 0.010 ; 0.019
REMARK 3 BOND LENGTHS OTHERS (A): NULL ; NULL ; NULL
REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 3537 ; 1.506 ; 2.006
REMARK 3 BOND ANGLES OTHERS (DEGREES): NULL ; NULL ; NULL
REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 326 ; 6.327 ; 5.000
REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 105 ;39.039 ;23.143
REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 390 ;11.684 ;15.000
REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 20 ;12.910 ;15.000
REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 401 ; 0.085 ; 0.200
REMARK 3 GENERAL PLANES REFINED ATOMS (A): 1996 ; 0.009 ; 0.022
REMARK 3 GENERAL PLANES OTHERS (A): NULL ; NULL ; NULL
REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): NULL ; NULL ; NULL
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): NULL ; NULL ; NULL
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): NULL ; NULL ; NULL
REMARK 3 SYMMETRY VDW OTHERS (A): NULL ; NULL ; NULL
REMARK 3 SYMMETRY H-BOND REFINED ATOMS (A): NULL ; NULL ; NULL
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): 1279 ; 1.675 ; 2.216
REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL
REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 1606 ; 2.235 ; 3.311
REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL
REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 1296 ; 2.134 ; 2.481
REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL
REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): NULL ; NULL ; NULL
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): 2575 ; 1.654 ; 3.000
REMARK 3 SPHERICITY; FREE ATOMS (A**2): 83 ;30.668 ; 5.000
REMARK 3 SPHERICITY; BONDED ATOMS (A**2): 2744 ;13.888 ; 5.000
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 : NULL
REMARK 3 PARAMETERS FOR MASK CALCULATION
REMARK 3 VDW PROBE RADIUS : 1.20
REMARK 3 ION PROBE RADIUS : 0.80
REMARK 3 SHRINKAGE RADIUS : 0.80
REMARK 3
REMARK 3 OTHER REFINEMENT REMARKS: HYDROGENS HAVE BEEN USED IF PRESENT IN
REMARK 3 THE INPUT U VALUES : REFINED INDIVIDUALLY
REMARK 4
REMARK 4 5K5B COMPLIES WITH FORMAT V. 3.30, 13-JUL-11
REMARK 100
REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 23-MAY-16.
REMARK 100 THE DEPOSITION ID IS D_1000221605.
REMARK 200
REMARK 200 EXPERIMENTAL DETAILS
REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION
REMARK 200 DATE OF DATA COLLECTION : 12-NOV-14
REMARK 200 TEMPERATURE (KELVIN) : 100
REMARK 200 PH : 4.95
REMARK 200 NUMBER OF CRYSTALS USED : 1
REMARK 200
REMARK 200 SYNCHROTRON (Y/N) : Y
REMARK 200 RADIATION SOURCE : ESRF
REMARK 200 BEAMLINE : ID23-1
REMARK 200 X-RAY GENERATOR MODEL : NULL
REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M
REMARK 200 WAVELENGTH OR RANGE (A) : 0.972957
REMARK 200 MONOCHROMATOR : SI(111)
REMARK 200 OPTICS : NULL
REMARK 200
REMARK 200 DETECTOR TYPE : PIXEL
REMARK 200 DETECTOR MANUFACTURER : DECTRIS PILATUS 6M-F
REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS
REMARK 200 DATA SCALING SOFTWARE : XSCALE OCT 15, 2015
REMARK 200
REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 75872
REMARK 200 RESOLUTION RANGE HIGH (A) : 1.350
REMARK 200 RESOLUTION RANGE LOW (A) : 46.970
REMARK 200 REJECTION CRITERIA (SIGMA(I)) : -3.000
REMARK 200
REMARK 200 OVERALL.
REMARK 200 COMPLETENESS FOR RANGE (%) : 98.1
REMARK 200 DATA REDUNDANCY : 4.360
REMARK 200 R MERGE (I) : 0.03600
REMARK 200 R SYM (I) : NULL
REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 18.3700
REMARK 200
REMARK 200 IN THE HIGHEST RESOLUTION SHELL.
REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.35
REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.38
REMARK 200 COMPLETENESS FOR SHELL (%) : 95.7
REMARK 200 DATA REDUNDANCY IN SHELL : 4.23
REMARK 200 R MERGE FOR SHELL (I) : 0.56000
REMARK 200 R SYM FOR SHELL (I) : NULL
REMARK 200 <I/SIGMA(I)> FOR SHELL : 2.310
REMARK 200
REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH
REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT
REMARK 200 SOFTWARE USED: PHASER 2.5.7
REMARK 200 STARTING MODEL: 4Q0H
REMARK 200
REMARK 200 REMARK: NULL
REMARK 280
REMARK 280 CRYSTAL
REMARK 280 SOLVENT CONTENT, VS (%): 48.66
REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.40
REMARK 280
REMARK 280 CRYSTALLIZATION CONDITIONS: SODIUM ACETATE, PEG 400, DTT, 2-METHYL
REMARK 280 -2, 4-PENTANEDIOL, PH 4.95, VAPOR DIFFUSION, HANGING DROP,
REMARK 280 TEMPERATURE 293K
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 46.88000
REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 27.14000
REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 0.00000
REMARK 290 SMTRY1 4 -1.000000 0.000000 0.000000 46.88000
REMARK 290 SMTRY2 4 0.000000 1.000000 0.000000 27.14000
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 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC
REMARK 350 SOFTWARE USED: PISA
REMARK 350 TOTAL BURIED SURFACE AREA: 5450 ANGSTROM**2
REMARK 350 SURFACE AREA OF THE COMPLEX: 27130 ANGSTROM**2
REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -56.0 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 0.00000
REMARK 350 BIOMT2 2 0.000000 1.000000 0.000000 0.00000
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 -13
REMARK 465 ALA A -12
REMARK 465 SER A -11
REMARK 465 MET A -10
REMARK 465 THR A -9
REMARK 465 GLY A -8
REMARK 465 GLY A -7
REMARK 465 GLN A -6
REMARK 465 GLN A -5
REMARK 465 MET A -4
REMARK 465 GLY A -3
REMARK 465 ARG A -2
REMARK 465 GLY A -1
REMARK 465 SER A 0
REMARK 465 MET A 1
REMARK 465 SER A 2
REMARK 465 ARG A 3
REMARK 465 ASP A 4
REMARK 465 PRO A 5
REMARK 465 LEU A 6
REMARK 465 ALA A 108
REMARK 465 ALA A 131
REMARK 465 TRP A 132
REMARK 465 ASP A 133
REMARK 465 SER A 134
REMARK 465 THR A 135
REMARK 465 GLY A 136
REMARK 465 PRO A 137
REMARK 465 HIS A 138
REMARK 465 ALA A 139
REMARK 465 GLU A 323
REMARK 465 HIS A 324
REMARK 465 HIS A 325
REMARK 465 HIS A 326
REMARK 465 HIS A 327
REMARK 465 HIS A 328
REMARK 465 HIS A 329
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 GLY A 109 N CA
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 ASN A 23 35.30 -147.48
REMARK 500 PRO A 106 72.55 -66.36
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 ACT A 402
REMARK 800
REMARK 800 SITE_IDENTIFIER: AC2
REMARK 800 EVIDENCE_CODE: SOFTWARE
REMARK 800 SITE_DESCRIPTION: binding site for residue ACT A 403
REMARK 800
REMARK 800 SITE_IDENTIFIER: AC3
REMARK 800 EVIDENCE_CODE: SOFTWARE
REMARK 800 SITE_DESCRIPTION: binding site for residue MPD A 404
REMARK 800
REMARK 800 SITE_IDENTIFIER: AC4
REMARK 800 EVIDENCE_CODE: SOFTWARE
REMARK 800 SITE_DESCRIPTION: binding site for residue LBV A 405
DBREF 5K5B A 1 321 UNP Q9RZA4 BPHY_DEIRA 1 321
SEQADV 5K5B MET A -13 UNP Q9RZA4 INITIATING METHIONINE
SEQADV 5K5B ALA A -12 UNP Q9RZA4 EXPRESSION TAG
SEQADV 5K5B SER A -11 UNP Q9RZA4 EXPRESSION TAG
SEQADV 5K5B MET A -10 UNP Q9RZA4 EXPRESSION TAG
SEQADV 5K5B THR A -9 UNP Q9RZA4 EXPRESSION TAG
SEQADV 5K5B GLY A -8 UNP Q9RZA4 EXPRESSION TAG
SEQADV 5K5B GLY A -7 UNP Q9RZA4 EXPRESSION TAG
SEQADV 5K5B GLN A -6 UNP Q9RZA4 EXPRESSION TAG
SEQADV 5K5B GLN A -5 UNP Q9RZA4 EXPRESSION TAG
SEQADV 5K5B MET A -4 UNP Q9RZA4 EXPRESSION TAG
SEQADV 5K5B GLY A -3 UNP Q9RZA4 EXPRESSION TAG
SEQADV 5K5B ARG A -2 UNP Q9RZA4 EXPRESSION TAG
SEQADV 5K5B GLY A -1 UNP Q9RZA4 EXPRESSION TAG
SEQADV 5K5B SER A 0 UNP Q9RZA4 EXPRESSION TAG
SEQADV 5K5B LEU A 322 UNP Q9RZA4 EXPRESSION TAG
SEQADV 5K5B GLU A 323 UNP Q9RZA4 EXPRESSION TAG
SEQADV 5K5B HIS A 324 UNP Q9RZA4 EXPRESSION TAG
SEQADV 5K5B HIS A 325 UNP Q9RZA4 EXPRESSION TAG
SEQADV 5K5B HIS A 326 UNP Q9RZA4 EXPRESSION TAG
SEQADV 5K5B HIS A 327 UNP Q9RZA4 EXPRESSION TAG
SEQADV 5K5B HIS A 328 UNP Q9RZA4 EXPRESSION TAG
SEQADV 5K5B HIS A 329 UNP Q9RZA4 EXPRESSION TAG
SEQRES 1 A 343 MET ALA SER MET THR GLY GLY GLN GLN MET GLY ARG GLY
SEQRES 2 A 343 SER MET SER ARG ASP PRO LEU PRO PHE PHE PRO PRO LEU
SEQRES 3 A 343 TYR LEU GLY GLY PRO GLU ILE THR THR GLU ASN CYS GLU
SEQRES 4 A 343 ARG GLU PRO ILE HIS ILE PRO GLY SER ILE GLN PRO HIS
SEQRES 5 A 343 GLY ALA LEU LEU THR ALA ASP GLY HIS SER GLY GLU VAL
SEQRES 6 A 343 LEU GLN MET SER LEU ASN ALA ALA THR PHE LEU GLY GLN
SEQRES 7 A 343 GLU PRO THR VAL LEU ARG GLY GLN THR LEU ALA ALA LEU
SEQRES 8 A 343 LEU PRO GLU GLN TRP PRO ALA LEU GLN ALA ALA LEU PRO
SEQRES 9 A 343 PRO GLY CYS PRO ASP ALA LEU GLN TYR ARG ALA THR LEU
SEQRES 10 A 343 ASP TRP PRO ALA ALA GLY HIS LEU SER LEU THR VAL HIS
SEQRES 11 A 343 ARG VAL GLY GLU LEU LEU ILE LEU GLU PHE GLU PRO THR
SEQRES 12 A 343 GLU ALA TRP ASP SER THR GLY PRO HIS ALA LEU ARG ASN
SEQRES 13 A 343 ALA MET PHE ALA LEU GLU SER ALA PRO ASN LEU ARG ALA
SEQRES 14 A 343 LEU ALA GLU VAL ALA THR GLN THR VAL ARG GLU LEU THR
SEQRES 15 A 343 GLY PHE ASP ARG VAL MET LEU TYR LYS PHE ALA PRO ASP
SEQRES 16 A 343 ALA THR GLY GLU VAL ILE ALA GLU ALA ARG ARG GLU GLY
SEQRES 17 A 343 LEU HIS ALA PHE LEU GLY HIS ARG PHE PRO ALA SER ASP
SEQRES 18 A 343 ILE PRO ALA GLN ALA ARG ALA LEU TYR THR ARG HIS LEU
SEQRES 19 A 343 LEU ARG LEU THR ALA ASP THR ARG ALA ALA ALA VAL PRO
SEQRES 20 A 343 LEU ASP PRO VAL LEU ASN PRO GLN THR ASN ALA PRO THR
SEQRES 21 A 343 PRO LEU GLY GLY ALA VAL LEU ARG ALA THR SER PRO MET
SEQRES 22 A 343 HIS MET GLN TYR LEU ARG ASN MET GLY VAL GLY SER SER
SEQRES 23 A 343 LEU SER VAL SER VAL VAL VAL GLY GLY GLN LEU TRP GLY
SEQRES 24 A 343 LEU ILE ALA CYS HIS HIS GLN THR PRO TYR VAL LEU PRO
SEQRES 25 A 343 PRO ASP LEU ARG THR THR LEU GLU TYR LEU GLY ARG LEU
SEQRES 26 A 343 LEU SER LEU GLN VAL GLN VAL LYS GLU ALA LEU GLU HIS
SEQRES 27 A 343 HIS HIS HIS HIS HIS
HET ACT A 401 4
HET ACT A 402 4
HET ACT A 403 4
HET MPD A 404 8
HET LBV A 405 43
HETNAM ACT ACETATE ION
HETNAM MPD (4S)-2-METHYL-2,4-PENTANEDIOL
HETNAM LBV 3-[2-[(Z)-[3-(2-CARBOXYETHYL)-5-[(Z)-(4-ETHENYL-3-
HETNAM 2 LBV METHYL-5-OXIDANYLIDENE-PYRROL-2-YLIDENE)METHYL]-4-
HETNAM 3 LBV METHYL-PYRROL-1-IUM -2-YLIDENE]METHYL]-5-[(Z)-[(3E)-3-
HETNAM 4 LBV ETHYLIDENE-4-METHYL-5-OXIDANYLIDENE-PYRROLIDIN-2-
HETNAM 5 LBV YLIDENE]METHYL]-4-METHYL-1H-PYRROL-3- YL]PROPANOIC
HETNAM 6 LBV ACID
HETSYN LBV 2(R),3(E)- PHYTOCHROMOBILIN
FORMUL 2 ACT 3(C2 H3 O2 1-)
FORMUL 5 MPD C6 H14 O2
FORMUL 6 LBV C33 H37 N4 O6 1+
FORMUL 7 HOH *322(H2 O)
HELIX 1 AA1 PRO A 11 GLY A 15 5 5
HELIX 2 AA2 ASN A 23 GLU A 27 5 5
HELIX 3 AA3 ASN A 57 GLY A 63 1 7
HELIX 4 AA4 GLU A 65 ARG A 70 1 6
HELIX 5 AA5 THR A 73 LEU A 78 1 6
HELIX 6 AA6 GLN A 81 LEU A 89 1 9
HELIX 7 AA7 ARG A 141 ALA A 150 1 10
HELIX 8 AA8 ASN A 152 GLY A 169 1 18
HELIX 9 AA9 PRO A 204 ILE A 208 5 5
HELIX 10 AB1 PRO A 209 HIS A 219 1 11
HELIX 11 AB2 SER A 257 MET A 267 1 11
HELIX 12 AB3 PRO A 298 LEU A 322 1 25
SHEET 1 AA1 7 SER A 34 ILE A 35 0
SHEET 2 AA1 7 VAL A 232 ASP A 235 -1 O VAL A 232 N ILE A 35
SHEET 3 AA1 7 VAL A 51 SER A 55 -1 N MET A 54 O ASP A 235
SHEET 4 AA1 7 ALA A 40 ASP A 45 -1 N THR A 43 O LEU A 52
SHEET 5 AA1 7 LEU A 121 THR A 129 -1 O LEU A 124 N LEU A 42
SHEET 6 AA1 7 HIS A 110 VAL A 118 -1 N SER A 112 O GLU A 127
SHEET 7 AA1 7 TYR A 99 LEU A 103 -1 N LEU A 103 O LEU A 111
SHEET 1 AA2 6 ARG A 202 PHE A 203 0
SHEET 2 AA2 6 GLY A 184 ARG A 191 -1 N GLY A 184 O PHE A 203
SHEET 3 AA2 6 ARG A 172 PHE A 178 -1 N LYS A 177 O GLU A 185
SHEET 4 AA2 6 GLN A 282 HIS A 291 -1 O ALA A 288 N MET A 174
SHEET 5 AA2 6 SER A 271 VAL A 279 -1 N LEU A 273 O CYS A 289
SHEET 6 AA2 6 LEU A 221 THR A 224 -1 N THR A 224 O SER A 272
LINK SG CYS A 24 CBA LBV A 405 1555 1555 1.67
CISPEP 1 ASP A 235 PRO A 236 0 -9.78
SITE 1 AC1 1 HOH A 707
SITE 1 AC2 4 ARG A 172 LEU A 195 HIS A 290 GLN A 292
SITE 1 AC3 6 PRO A 258 MET A 259 GLN A 262 HOH A 601
SITE 2 AC3 6 HOH A 614 HOH A 726
SITE 1 AC4 24 CYS A 24 MET A 174 TYR A 176 PHE A 198
SITE 2 AC4 24 PHE A 203 ASP A 207 ILE A 208 PRO A 209
SITE 3 AC4 24 TYR A 216 ARG A 254 THR A 256 SER A 257
SITE 4 AC4 24 HIS A 260 TYR A 263 SER A 272 SER A 274
SITE 5 AC4 24 HIS A 290 HOH A 513 HOH A 560 HOH A 561
SITE 6 AC4 24 HOH A 562 HOH A 574 HOH A 675 HOH A 680
CRYST1 93.760 54.280 70.150 90.00 92.20 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 0.010666 0.000000 0.000410 0.00000
SCALE2 0.000000 0.018423 0.000000 0.00000
SCALE3 0.000000 0.000000 0.014266 0.00000
(ATOM LINES ARE NOT SHOWN.)
END
