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- PDB-5ewu: Crystal structure of the Arabidopsis thaliana C-terminal Chlh at 1.25A -

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Basic information

Entry
Database: PDB / ID: 5ewu
TitleCrystal structure of the Arabidopsis thaliana C-terminal Chlh at 1.25A
ComponentsMagnesium-chelatase subunit ChlH, chloroplastic
KeywordsLIGASE / MG-CHELATASE / GUN5 / METAL BINDING PROTEIN / Magnesium-chelatase subunit ChlH / ABAR / CCH / RTL1
Function / homology
Function and homology information


magnesium chelatase complex / magnesium chelatase / magnesium chelatase activity / chloroplast inner membrane / chlorophyll biosynthetic process / plastid / chloroplast stroma / photosynthesis / chloroplast / mRNA binding ...magnesium chelatase complex / magnesium chelatase / magnesium chelatase activity / chloroplast inner membrane / chlorophyll biosynthetic process / plastid / chloroplast stroma / photosynthesis / chloroplast / mRNA binding / mitochondrion / 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
BENZOIC ACID / Magnesium-chelatase subunit ChlH, chloroplastic
Similarity search - Component
Biological speciesArabidopsis thaliana (thale cress)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 1.25 Å
AuthorsChen, Z. / Zhang, X. / Liu, Y. / Jiang, L.
CitationJournal: To Be Published
Title: Crystal structure of the Arabidopsis thaliana C-terminal Chlh at 1.25A
Authors: Chen, Z. / Zhang, X. / Liu, Y. / Jiang, L.
History
DepositionNov 21, 2015Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Dec 7, 2016Provider: repository / Type: Initial release
Revision 1.1Feb 19, 2020Group: Data collection / Category: diffrn_source / Item: _diffrn_source.pdbx_synchrotron_site
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_conn_angle / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Magnesium-chelatase subunit ChlH, chloroplastic
B: Magnesium-chelatase subunit ChlH, chloroplastic
hetero molecules


Theoretical massNumber of molelcules
Total (without water)87,8989
Polymers87,5322
Non-polymers3667
Water22,1221228
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2590 Å2
ΔGint-42 kcal/mol
Surface area29940 Å2
Unit cell
Length a, b, c (Å)69.099, 72.776, 72.911
Angle α, β, γ (deg.)90.00, 109.76, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Magnesium-chelatase subunit ChlH, chloroplastic / Mg-chelatase subunit H / ABA-binding protein / Mg-protoporphyrin IX chelatase subunit ChlH / ...Mg-chelatase subunit H / ABA-binding protein / Mg-protoporphyrin IX chelatase subunit ChlH / Protein CONDITIONAL CHLORINA / Protein GENOMES UNCOUPLED 5 / Protein RAPID TRANSPIRATION IN DETACHED LEAVES 1


Mass: 43765.984 Da / Num. of mol.: 2 / Fragment: UNP residues 994-1381
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Arabidopsis thaliana (thale cress) / Gene: CHLH, ABAR, CCH, GUN5, RTL1, At5g13630, MSH12.9 / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 / References: UniProt: Q9FNB0, magnesium chelatase
#2: Chemical ChemComp-BEZ / BENZOIC ACID


Mass: 122.121 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C7H6O2
#3: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: Mg
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1228 / 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: 1.97 Å3/Da / Density % sol: 37.6 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 7 / Details: PEG, NaCl

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: AR-NE3A / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Jun 4, 2009
RadiationProtocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.25→50 Å / Num. all: 187584 / Num. obs: 168362 / % possible obs: 89.8 % / Redundancy: 5.9 % / Net I/σ(I): 45

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Processing

Software
NameVersionClassification
REFMAC5.5.0109refinement
HKL-2000data reduction
HKL-2000data scaling
SHARPphasing
RefinementResolution: 1.25→50 Å / Cor.coef. Fo:Fc: 0.967 / Cor.coef. Fo:Fc free: 0.962 / SU B: 1.458 / SU ML: 0.029 / Cross valid method: THROUGHOUT / ESU R: 0.061 / ESU R Free: 0.051 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.18404 8308 4.9 %RANDOM
Rwork0.16895 ---
obs0.16971 159967 89.79 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 19.411 Å2
Baniso -1Baniso -2Baniso -3
1-0.2 Å20 Å20.85 Å2
2--1.04 Å20 Å2
3----0.67 Å2
Refinement stepCycle: LAST / Resolution: 1.25→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5843 0 23 1232 7098
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0226026
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.1541.9538178
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.3635779
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.23324.771262
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.684151039
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.3311537
X-RAY DIFFRACTIONr_chiral_restr0.0810.2934
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0214529
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.8821.53822
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.54426144
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it2.18332204
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it3.3784.52024
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr0.91936026
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.25→1.282 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.346 310 -
Rwork0.363 5972 -
obs--45.38 %

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