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- PDB-4zhj: Crystal Structure of the Catalytic Subunit of Magnesium Chelatase -

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Basic information

Entry
Database: PDB / ID: 4zhj
TitleCrystal Structure of the Catalytic Subunit of Magnesium Chelatase
ComponentsMg-chelatase subunit ChlH
KeywordsMETAL BINDING PROTEIN / Mg-chelatase / GUN5
Function / homology
Function and homology information


magnesium chelatase / magnesium chelatase activity / chlorophyll biosynthetic process / photosynthesis / ATP binding
Similarity search - Function
Magnesium-chelatase, subunit H / Magnesium chelatase, subunit H, N-terminal / Domain of unknown function (DUF3479) / CobN/magnesium chelatase / CobN/Magnesium Chelatase
Similarity search - Domain/homology
Biological speciesSynechocystis sp. PCC 6803 substr. Kazusa (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.502 Å
AuthorsChen, X. / Pu, H. / Fang, Y. / Liu, L.
CitationJournal: Nat.Plants / Year: 2015
Title: Crystal structure of the catalytic subunit of magnesium chelatase
Authors: Chen, X. / Pu, H. / Fang, Y. / Wang, X. / Zhao, S. / Lin, Y. / Zhang, M. / Dai, H.E. / Gong, W. / Liu, L.
History
DepositionApr 25, 2015Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Aug 26, 2015Provider: repository / Type: Initial release
Revision 1.1Jun 15, 2016Group: Database references
Revision 1.2Mar 20, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_oper_list
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_oper_list.symmetry_operation

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Mg-chelatase subunit ChlH
B: Mg-chelatase subunit ChlH


Theoretical massNumber of molelcules
Total (without water)301,7432
Polymers301,7432
Non-polymers00
Water15,853880
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3620 Å2
ΔGint-11 kcal/mol
Surface area88130 Å2
MethodPISA
Unit cell
Length a, b, c (Å)319.717, 319.717, 105.194
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number146
Space group name H-MH3

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Components

#1: Protein Mg-chelatase subunit ChlH


Mass: 150871.500 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Synechocystis sp. PCC 6803 substr. Kazusa (bacteria)
Strain: PCC 6803 substr. Kazusa / Gene: chlH / Production host: Escherichia coli (E. coli) / References: UniProt: P73020
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 880 / 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: 3.48 Å3/Da / Density % sol: 64.65 %
Crystal growTemperature: 289 K / Method: vapor diffusion, hanging drop / pH: 7 / Details: 0.85 M sodium citrate, 2 mM dithiothreitol

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 0.9793 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Apr 11, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9793 Å / Relative weight: 1
ReflectionResolution: 2.5→50 Å / Num. obs: 138183 / % possible obs: 99.99 % / Redundancy: 4.1 % / Rmerge(I) obs: 0.085 / Rsym value: 0.085 / Net I/σ(I): 16.7
Reflection shellResolution: 2.5→2.59 Å / Redundancy: 4.1 % / Rmerge(I) obs: 0.82 / Mean I/σ(I) obs: 2.3 / % possible all: 100

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Phasing

PhasingMethod: SAD

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Processing

Software
NameVersionClassification
HKL-2000data collection
SCALEPACKdata scaling
SHELXphasing
PHENIX(phenix.refine: 1.8.1_1168)refinement
PDB_EXTRACT3.15data extraction
HKL-2000data reduction
RefinementMethod to determine structure: SAD / Resolution: 2.502→44.959 Å / FOM work R set: 0.8563 / SU ML: 0.28 / Cross valid method: FREE R-VALUE / σ(F): 1.97 / Phase error: 22.08 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2092 6733 5.01 %
Rwork0.1774 127632 -
obs0.179 134365 97.11 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 148.79 Å2 / Biso mean: 49.29 Å2 / Biso min: 19.1 Å2
Refinement stepCycle: final / Resolution: 2.502→44.959 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms19238 0 0 880 20118
Biso mean---47.94 -
Num. residues----2491
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00319688
X-RAY DIFFRACTIONf_angle_d0.87326769
X-RAY DIFFRACTIONf_chiral_restr0.0583016
X-RAY DIFFRACTIONf_plane_restr0.0043503
X-RAY DIFFRACTIONf_dihedral_angle_d13.6197204
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 30

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.5017-2.53010.30441510.26152756290764
2.5301-2.55990.33711570.25793325348276
2.5599-2.59110.31381680.2433809397786
2.5911-2.62390.2922390.2344143438294
2.6239-2.65840.27561940.23884274446898
2.6584-2.69480.25952560.23743894645100
2.6948-2.73330.26842100.237143544564100
2.7333-2.77410.30972320.221443894621100
2.7741-2.81740.2732470.21343514598100
2.8174-2.86360.23912290.200343934622100
2.8636-2.9130.23462470.197643264573100
2.913-2.9660.23752160.20343914607100
2.966-3.0230.24772410.201644134654100
3.023-3.08470.22142290.196243964625100
3.0847-3.15170.24582000.197743484548100
3.1517-3.2250.21762400.189644314671100
3.225-3.30570.21522510.190743734624100
3.3057-3.3950.2192450.176943624607100
3.395-3.49490.20292260.169143744600100
3.4949-3.60760.20392230.162943964619100
3.6076-3.73650.20092300.162843834613100
3.7365-3.8860.17912300.159843644594100
3.886-4.06280.17082270.15143774604100
4.0628-4.27680.19552450.143943704615100
4.2768-4.54450.15022320.13943814613100
4.5445-4.8950.16872200.1443904610100
4.895-5.38690.18232440.158443494593100
5.3869-6.16470.19422250.181243914616100
6.1647-7.76040.22432640.179643184582100
7.7604-44.96620.16132150.15844316453198
Refinement TLS params.Method: refined / Origin x: -15.7507 Å / Origin y: 63.7626 Å / Origin z: -4.4732 Å
111213212223313233
T0.2577 Å20.0476 Å20.0203 Å2-0.258 Å20.0142 Å2--0.2481 Å2
L0.0883 °2-0.0499 °20.0027 °2-0.2621 °20.2413 °2--0.6046 °2
S0.0125 Å °-0.0264 Å °0.01 Å °-0.0206 Å °0.0281 Å °-0.0161 Å °-0.052 Å °0.1656 Å °-0.0403 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1allA0 - 1330
2X-RAY DIFFRACTION1allB-1 - 1328
3X-RAY DIFFRACTION1allS1 - 880

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