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- PDB-4eoc: Crystal structure of h74q Synechocystis sp. PCYA -

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Basic information

Entry
Database: PDB / ID: 4eoc
TitleCrystal structure of h74q Synechocystis sp. PCYA
ComponentsPhycocyanobilin:ferredoxin oxidoreductase
KeywordsOXIDOREDUCTASE / ALPHA-BETA-ALPHA SANDWICH / RADICAL CHEMISTRY
Function / homology
Function and homology information


phycocyanobilin:ferredoxin oxidoreductase / phycocyanobilin:ferredoxin oxidoreductase activity / phytochromobilin:ferredoxin oxidoreductase activity / phytochromobilin biosynthetic process / cobalt ion binding
Similarity search - Function
Phycocyanobilin:ferredoxin oxidoreductase / oxygen-dependent coproporphyrinogen oxidase - #20 / Ferredoxin-dependent bilin reductase / Ferredoxin-dependent bilin reductase / oxygen-dependent coproporphyrinogen oxidase / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
BILIVERDINE IX ALPHA / Phycocyanobilin:ferredoxin oxidoreductase
Similarity search - Component
Biological speciesSynechocystis sp. PCC 6803 substr. Kazusa (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.49 Å
AuthorsKabasakal, B.V. / Fisher, A.J.
CitationJournal: To be Published
Title: Crystal structure of h74q Synechocystis sp. PCYA
Authors: Kabasakal, B.V. / Gae, D.D. / Fisher, A.J.
History
DepositionApr 13, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 29, 2012Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Phycocyanobilin:ferredoxin oxidoreductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,8574
Polymers27,2031
Non-polymers6543
Water5,585310
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)70.400, 94.880, 42.570
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212

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Components

#1: Protein Phycocyanobilin:ferredoxin oxidoreductase


Mass: 27203.016 Da / Num. of mol.: 1 / Fragment: unp residues 8-246 / Mutation: H74Q
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Synechocystis sp. PCC 6803 substr. Kazusa (bacteria)
Strain: PCC6803 / Gene: pcyA, slr0116 / Plasmid: pTYB12 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21
References: UniProt: Q55891, phycocyanobilin:ferredoxin oxidoreductase
#2: Chemical ChemComp-BLA / BILIVERDINE IX ALPHA


Mass: 582.646 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C33H34N4O6
#3: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 310 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.61 Å3/Da / Density % sol: 52.93 %
Crystal growTemperature: 298 K / Method: vapor diffusion / pH: 7
Details: 1-1.25 M sodium citrate, 0.1-0.4 M NaCl in 0.1 M Tris HCl, pH 7, VAPOR DIFFUSION, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL7-1 / Wavelength: 0.97946 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Feb 14, 2011 / Details: Si(111)
RadiationMonochromator: Side scattering I-beam bent single crystal; asymmetric cut 4.9650 deg
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97946 Å / Relative weight: 1
ReflectionResolution: 1.49→50 Å / Num. all: 46661 / Num. obs: 46661 / % possible obs: 98.6 % / Observed criterion σ(F): -3 / Observed criterion σ(I): -3 / Redundancy: 3.51 % / Biso Wilson estimate: 19.43 Å2 / Rmerge(I) obs: 0.03 / Rsym value: 0.03 / Net I/σ(I): 21.7
Reflection shellResolution: 1.49→1.53 Å / Redundancy: 3.41 % / Rmerge(I) obs: 0.447 / Mean I/σ(I) obs: 2.7 / Num. unique all: 3356 / Rsym value: 0.447 / % possible all: 96.2

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Processing

Software
NameVersionClassification
Blu-Icedata collection
PHASERphasing
REFMAC5.5.0109refinement
XDSdata reduction
XSCALEdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.49→38.84 Å / Cor.coef. Fo:Fc: 0.965 / Cor.coef. Fo:Fc free: 0.951 / SU B: 2.435 / SU ML: 0.044 / Cross valid method: THROUGHOUT / ESU R: 0.071 / ESU R Free: 0.073 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.2072 2354 5 %RANDOM
Rwork0.17951 ---
obs0.1809 44307 98.57 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 21.478 Å2
Baniso -1Baniso -2Baniso -3
1--1.19 Å20 Å20 Å2
2--1.32 Å20 Å2
3----0.13 Å2
Refine analyzeLuzzati coordinate error obs: 0.071 Å / Luzzati sigma a obs: 0.044 Å
Refinement stepCycle: LAST / Resolution: 1.49→38.84 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1911 0 45 310 2266
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0222108
X-RAY DIFFRACTIONr_angle_refined_deg1.6332.0032886
X-RAY DIFFRACTIONr_dihedral_angle_1_deg14.6065.074272
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.98624.902102
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.02915366
X-RAY DIFFRACTIONr_dihedral_angle_4_deg11.6731513
X-RAY DIFFRACTIONr_chiral_restr0.0940.2305
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.0211664
X-RAY DIFFRACTIONr_mcbond_it0.7791.51258
X-RAY DIFFRACTIONr_mcangle_it1.41322048
X-RAY DIFFRACTIONr_scbond_it2.2323850
X-RAY DIFFRACTIONr_scangle_it3.6044.5825
LS refinement shellResolution: 1.491→1.53 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.268 156 -
Rwork0.29 3191 -
obs--96.04 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
147.90979.0353-25.71276.9383-4.606318.59311.22851.65641.292-0.1137-0.3370.856-1.1663-1.0838-0.89150.09230.0827-0.05430.14010.08930.1433-15.80236.841-31.637
21.62880.42680.19870.66560.29490.32010.0064-0.02760.1838-0.0624-0.00880.0316-0.0062-0.04950.00240.00840.0045-0.00150.024-0.00360.0708-11.19833.094-22.212
32.0761-0.1876-0.31560.39760.10960.55190.0343-0.0513-0.26880.028-0.021-0.00050.0792-0.0479-0.01340.0199-0.0079-0.01480.0070.01750.0962-9.33115.395-18.858
41.14630.7426-0.4621.1102-0.74191.44030.0115-0.18990.14880.1250.0307-0.1011-0.0063-0.1677-0.04220.051-0.0007-0.02180.1024-0.01560.0807-4.97731.914-9.343
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A5 - 13
2X-RAY DIFFRACTION2A14 - 112
3X-RAY DIFFRACTION3A113 - 193
4X-RAY DIFFRACTION4A194 - 246

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