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- PDB-4ykb: Structure of GUN4 from Chlamydomonas reinhardtii -

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Basic information

Entry
Database: PDB / ID: 4ykb
TitleStructure of GUN4 from Chlamydomonas reinhardtii
ComponentsTetrapyrrole-binding protein
KeywordsPLANT PROTEIN
Function / homologychloroplast-nucleus signaling pathway / GUN4-like / GUN4-like superfamily / GUN4-like / tetrapyrrole binding / chloroplast / enzyme binding / Tetrapyrrole-binding protein
Function and homology information
Biological speciesChlamydomonas reinhardtii (plant)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.5 Å
AuthorsTabriz, S.T. / Langley, D.B. / Willows, R.D. / Duff, A.P. / Harrop, S.J.
CitationJournal: Acta Crystallogr F Struct Biol Commun / Year: 2015
Title: Structure of GUN4 from Chlamydomonas reinhardtii.
Authors: Tarahi Tabrizi, S. / Langley, D.B. / Harrop, S.J. / Duff, A.P. / Willows, R.D.
History
DepositionMar 4, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 12, 2015Provider: repository / Type: Initial release
Revision 1.1May 16, 2018Group: Data collection / Database references / Derived calculations
Category: citation / citation_author ...citation / citation_author / diffrn_source / pdbx_struct_oper_list
Item: _citation.journal_abbrev / _citation.journal_id_ASTM ..._citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_ISSN / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.name / _diffrn_source.pdbx_synchrotron_site / _pdbx_struct_oper_list.symmetry_operation
Revision 1.2Sep 27, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
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: Tetrapyrrole-binding protein
B: Tetrapyrrole-binding protein
C: Tetrapyrrole-binding protein
D: Tetrapyrrole-binding protein
E: Tetrapyrrole-binding protein
F: Tetrapyrrole-binding protein


Theoretical massNumber of molelcules
Total (without water)154,9386
Polymers154,9386
Non-polymers00
Water0
1
A: Tetrapyrrole-binding protein


Theoretical massNumber of molelcules
Total (without water)25,8231
Polymers25,8231
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Tetrapyrrole-binding protein


Theoretical massNumber of molelcules
Total (without water)25,8231
Polymers25,8231
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: Tetrapyrrole-binding protein


Theoretical massNumber of molelcules
Total (without water)25,8231
Polymers25,8231
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
4
D: Tetrapyrrole-binding protein


Theoretical massNumber of molelcules
Total (without water)25,8231
Polymers25,8231
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
5
E: Tetrapyrrole-binding protein


Theoretical massNumber of molelcules
Total (without water)25,8231
Polymers25,8231
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
6
F: Tetrapyrrole-binding protein


Theoretical massNumber of molelcules
Total (without water)25,8231
Polymers25,8231
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)114.998, 114.998, 141.193
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Space group name H-MP3221
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
12A
22C
13A
23D
14A
24E
15A
25F
16B
26C
17B
27D
18B
28E
19B
29F
110C
210D
111C
211E
112C
212F
113D
213E
114D
214F
115E
215F

NCS domain segments:
Dom-IDComponent-IDEns-IDRefine codeAuth asym-IDAuth seq-ID
1010A82 - 236
2010B82 - 236
1020A82 - 235
2020C82 - 235
1030A82 - 236
2030D82 - 236
1040A83 - 235
2040E83 - 235
1050A83 - 233
2050F83 - 233
1060B82 - 236
2060C82 - 236
1070B82 - 236
2070D82 - 236
1080B83 - 236
2080E83 - 236
1090B83 - 234
2090F83 - 234
10100C82 - 236
20100D82 - 236
10110C83 - 236
20110E83 - 236
10120C83 - 233
20120F83 - 233
10130D83 - 236
20130E83 - 236
10140D83 - 234
20140F83 - 234
10150E83 - 234
20150F83 - 234

NCS ensembles :
ID
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15

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Components

#1: Protein
Tetrapyrrole-binding protein


Mass: 25823.041 Da / Num. of mol.: 6 / Fragment: residues 40-260
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Chlamydomonas reinhardtii (plant) / Gene: GUN4, CHLREDRAFT_205768 / Production host: Escherichia coli (E. coli) / References: UniProt: A8I5N5

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.64 Å3/Da / Density % sol: 53 % / Description: very small hexagonal rods
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8
Details: 1:1 ratio of protein (35 mg/mL in 20 mM Tricine (pH 8.0), 2 mM beta-mercaptoethanol) to well solution (1.0 M ammonium citrate (pH 7.0), 0.1 M Bis Tris Propane (pH 7.0). Crystals only ...Details: 1:1 ratio of protein (35 mg/mL in 20 mM Tricine (pH 8.0), 2 mM beta-mercaptoethanol) to well solution (1.0 M ammonium citrate (pH 7.0), 0.1 M Bis Tris Propane (pH 7.0). Crystals only appeared after 44 weeks, likely the time taken for proteolysis, resulting in the N- and C-terminal truncations
PH range: 7.0-8.0

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX2 / Wavelength: 0.9537 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jun 20, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9537 Å / Relative weight: 1
ReflectionResolution: 3.5→44.56 Å / Num. obs: 13965 / % possible obs: 99.1 % / Redundancy: 3.5 % / Biso Wilson estimate: 78 Å2 / Rmerge(I) obs: 0.21 / Net I/σ(I): 5.2
Reflection shellResolution: 3.5→3.83 Å / Redundancy: 3.6 % / Rmerge(I) obs: 0.666 / Mean I/σ(I) obs: 1.9 / % possible all: 99

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Processing

Software
NameVersionClassification
REFMAC5.8.0103refinement
MOSFLMdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1Z3X

1z3x


Resolution: 3.5→44.5 Å / Cor.coef. Fo:Fc: 0.879 / Cor.coef. Fo:Fc free: 0.813 / SU B: 43.036 / SU ML: 0.663 / Cross valid method: THROUGHOUT / ESU R Free: 0.77 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.31315 753 5.4 %RANDOM
Rwork0.25602 ---
obs0.25907 13187 99.05 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 57.378 Å2
Baniso -1Baniso -2Baniso -3
1--0.55 Å2-0.28 Å20 Å2
2---0.55 Å20 Å2
3---1.79 Å2
Refinement stepCycle: LAST / Resolution: 3.5→44.5 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6241 0 0 0 6241
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0196406
X-RAY DIFFRACTIONr_bond_other_d0.0070.025416
X-RAY DIFFRACTIONr_angle_refined_deg1.4661.9088807
X-RAY DIFFRACTIONr_angle_other_deg1.578312180
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.3525861
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.42923.493229
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.21915702
X-RAY DIFFRACTIONr_dihedral_angle_4_deg12.2381517
X-RAY DIFFRACTIONr_chiral_restr0.0880.21039
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.027473
X-RAY DIFFRACTIONr_gen_planes_other0.0050.021544
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_it3.9796.2873495
X-RAY DIFFRACTIONr_mcbond_other3.9786.2873494
X-RAY DIFFRACTIONr_mcangle_it6.3899.4234339
X-RAY DIFFRACTIONr_mcangle_other6.3889.4234340
X-RAY DIFFRACTIONr_scbond_it3.9996.5742911
X-RAY DIFFRACTIONr_scbond_other3.9986.5742912
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other6.4399.7544469
X-RAY DIFFRACTIONr_long_range_B_refined12.07960.55327297
X-RAY DIFFRACTIONr_long_range_B_other12.07960.55327298
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Weight position: 0.05

Ens-IDDom-IDAuth asym-IDNumberRms dev position (Å)
11A129920.06
12B129920.06
21A135260.06
22C135260.06
31A130700.05
32D130700.05
41A129800.06
42E129800.06
51A117000.05
52F117000.05
61B132740.07
62C132740.07
71B130080.06
72D130080.06
81B127360.06
82E127360.06
91B115940.06
92F115940.06
101C131880.06
102D131880.06
111C129560.06
112E129560.06
121C120880.06
122F120880.06
131D125820.06
132E125820.06
141D118840.06
142F118840.06
151E115240.07
152F115240.07
LS refinement shellResolution: 3.5→3.588 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.377 44 -
Rwork0.316 955 -
obs--98.62 %

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