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- PDB-5dqr: The crystal structure of Arabidopsis 7-hydroxymethyl chlorophyll ... -

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Basic information

Entry
Database: PDB / ID: 5dqr
TitleThe crystal structure of Arabidopsis 7-hydroxymethyl chlorophyll a reductase (HCAR)
Components7-hydroxymethyl chlorophyll a reductase, chloroplastic
KeywordsOXIDOREDUCTASE / iron-sulfur flavoenzyme / HCAR / chlorophyll cycle
Function / homology
Function and homology information


7-hydroxymethyl chlorophyll a reductase / chlorophyll cycle / 7-hydroxymethyl chlorophyll a reductase activity / chlorophyll metabolic process / iron-sulfur cluster binding / chloroplast / extracellular region / metal ion binding
Similarity search - Function
Coenzyme F420 hydrogenase/dehydrogenase beta subunit, N-terminal / Coenzyme F420 hydrogenase/dehydrogenase beta subunit, C-terminal / Oxidoreductase FRHB/FDHB/HCAR-like / Coenzyme F420 hydrogenase/dehydrogenase, beta subunit N-term / Coenzyme F420 hydrogenase/dehydrogenase, beta subunit C terminus
Similarity search - Domain/homology
FLAVIN-ADENINE DINUCLEOTIDE / IRON/SULFUR CLUSTER / 7-hydroxymethyl chlorophyll a reductase, chloroplastic
Similarity search - Component
Biological speciesArabidopsis thaliana (thale cress)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.7 Å
AuthorsWang, X. / Liu, L.
CitationJournal: J.Biol.Chem. / Year: 2016
Title: Crystal Structure and Catalytic Mechanism of 7-Hydroxymethyl Chlorophyll a Reductase
Authors: Wang, X. / Liu, L.
History
DepositionSep 15, 2015Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Apr 20, 2016Provider: repository / Type: Initial release
Revision 1.1Jun 29, 2016Group: Database references
Revision 1.2Sep 27, 2017Group: Data collection / Database references / Derived calculations
Category: citation / diffrn_detector / pdbx_struct_oper_list
Item: _citation.journal_id_CSD / _diffrn_detector.detector / _pdbx_struct_oper_list.symmetry_operation
Revision 1.3Mar 20, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: 7-hydroxymethyl chlorophyll a reductase, chloroplastic
B: 7-hydroxymethyl chlorophyll a reductase, chloroplastic
C: 7-hydroxymethyl chlorophyll a reductase, chloroplastic
D: 7-hydroxymethyl chlorophyll a reductase, chloroplastic
E: 7-hydroxymethyl chlorophyll a reductase, chloroplastic
F: 7-hydroxymethyl chlorophyll a reductase, chloroplastic
hetero molecules


Theoretical massNumber of molelcules
Total (without water)303,34224
Polymers294,4096
Non-polymers8,93318
Water11,205622
1
A: 7-hydroxymethyl chlorophyll a reductase, chloroplastic
B: 7-hydroxymethyl chlorophyll a reductase, chloroplastic
C: 7-hydroxymethyl chlorophyll a reductase, chloroplastic
hetero molecules


Theoretical massNumber of molelcules
Total (without water)151,67112
Polymers147,2053
Non-polymers4,4669
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9890 Å2
ΔGint-206 kcal/mol
Surface area48160 Å2
MethodPISA
2
D: 7-hydroxymethyl chlorophyll a reductase, chloroplastic
E: 7-hydroxymethyl chlorophyll a reductase, chloroplastic
F: 7-hydroxymethyl chlorophyll a reductase, chloroplastic
hetero molecules


Theoretical massNumber of molelcules
Total (without water)151,67112
Polymers147,2053
Non-polymers4,4669
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area10190 Å2
ΔGint-208 kcal/mol
Surface area46370 Å2
MethodPISA
Unit cell
Length a, b, c (Å)89.105, 89.105, 273.312
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number145
Space group name H-MP32

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Components

#1: Protein
7-hydroxymethyl chlorophyll a reductase, chloroplastic


Mass: 49068.238 Da / Num. of mol.: 6 / Fragment: UNP residues 26-462
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Arabidopsis thaliana (thale cress) / Gene: HCAR, HMCR, At1g04620, T1G11.13 / Production host: Escherichia coli (E. coli)
References: UniProt: Q8GS60, 7-hydroxymethyl chlorophyll a reductase
#2: Chemical
ChemComp-SF4 / IRON/SULFUR CLUSTER


Mass: 351.640 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: Fe4S4
#3: Chemical
ChemComp-FAD / FLAVIN-ADENINE DINUCLEOTIDE


Mass: 785.550 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C27H33N9O15P2 / Comment: FAD*YM
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 622 / 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: 2.21 Å3/Da / Density % sol: 44.45 %
Description: THE ENTRY CONTAINS FRIEDEL PAIRS IN F_PLUS/MINUS COLUMNS.
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: 0.2M MgCl2, 0.1M Tris-HCl pH 8.5, 25%PEG3350(w/v), 3% EG(v/v)

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 0.9793 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Apr 21, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9793 Å / Relative weight: 1
ReflectionResolution: 2.7→50 Å / Num. obs: 66528 / % possible obs: 99.6 % / Redundancy: 3.2 % / Rmerge(I) obs: 0.079 / Rsym value: 0.052 / Net I/σ(I): 11.6
Reflection shellResolution: 2.7→2.8 Å / Redundancy: 3.2 % / Rmerge(I) obs: 0.512 / Mean I/σ(I) obs: 2.3 / Rejects: 0 / % possible all: 99.9

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Processing

Software
NameVersionClassification
PHENIXrefinement
PDB_EXTRACT3.15data extraction
PHENIXmodel building
PHENIXphasing
HKL-2000data scaling
HKL-2000data reduction
HKL-2000data processing
RefinementMethod to determine structure: SAD / Resolution: 2.7→44.61 Å / SU ML: 0.34 / Cross valid method: FREE R-VALUE / σ(F): 1.97 / Phase error: 25.51 / Stereochemistry target values: ML
Details: SF FILE CONTAINS FRIEDEL PAIRS UNDER I/F_MINUS AND I/F_PLUS COLUMNS.
RfactorNum. reflection% reflection
Rfree0.246 3318 5.09 %
Rwork0.202 61927 -
obs0.204 65245 97.7 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 71.23 Å2 / Biso mean: 17.02 Å2 / Biso min: 0.77 Å2
Refinement stepCycle: final / Resolution: 2.7→44.61 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms19252 0 414 622 20288
Biso mean--8.32 13.9 -
Num. residues----2476
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 24

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.6976-2.73620.33381110.27211934204575
2.7362-2.7770.3241420.26192360250288
2.777-2.82040.34741210.26142490261195
2.8204-2.86660.32561460.25292641278799
2.8666-2.9160.27241340.252226212755100
2.916-2.96910.30721550.245726692824100
2.9691-3.02610.27931560.252925962752100
3.0261-3.08790.3141470.249126262773100
3.0879-3.1550.29721400.245526262766100
3.155-3.22840.29331370.235826512788100
3.2284-3.30910.28881620.228626222784100
3.3091-3.39860.27861540.223126072761100
3.3986-3.49850.26131340.217526422776100
3.4985-3.61140.26261240.213726642788100
3.6114-3.74040.23241390.19542625276499
3.7404-3.89010.2341390.192626362775100
3.8901-4.0670.22551330.18032649278299
4.067-4.28130.22411430.175226302773100
4.2813-4.54930.19621040.15832636274099
4.5493-4.90010.1791290.159926622791100
4.9001-5.39250.23681440.18472589273399
5.3925-6.1710.21391450.19172633277899
6.171-7.76820.21821310.18272600273198
7.7682-44.61130.19661480.16842518266696

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