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- PDB-4rth: The crystal structure of PsbP from Zea mays -

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Basic information

Entry
Database: PDB / ID: 4rth
TitleThe crystal structure of PsbP from Zea mays
ComponentsMembrane-extrinsic protein of photosystem II PsbP
KeywordsPHOTOSYNTHESIS / beta-sandwich folding / membrane-extrinsic protein of photosystem II
Function / homologyMog1/PsbP, alpha/beta/alpha sandwich / Protein Transport Mog1p; Chain A / 3-Layer(aba) Sandwich / Alpha Beta / :
Function and homology information
Biological speciesZea mays (maize)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.6 Å
AuthorsCao, P. / Xie, Y. / Li, M. / Pan, X.W. / Zhang, H.M. / Zhao, X.L. / Su, X.D. / Cheng, T. / Chang, W.
CitationJournal: Mol Plant / Year: 2015
Title: Crystal structure analysis of extrinsic PsbP protein of photosystem II reveals a manganese-induced conformational change.
Authors: Cao, P. / Xie, Y. / Li, M. / Pan, X. / Zhang, H. / Zhao, X. / Su, X. / Cheng, T. / Chang, W.
History
DepositionNov 15, 2014Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Mar 11, 2015Provider: repository / Type: Initial release
Revision 1.1Aug 24, 2022Group: Database references / Category: citation / citation_author / database_2
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.title / _citation_author.name / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.2Nov 8, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model / struct_ncs_dom_lim
Item: _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id ..._struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Membrane-extrinsic protein of photosystem II PsbP
B: Membrane-extrinsic protein of photosystem II PsbP


Theoretical massNumber of molelcules
Total (without water)40,3072
Polymers40,3072
Non-polymers00
Water4,792266
1
A: Membrane-extrinsic protein of photosystem II PsbP


Theoretical massNumber of molelcules
Total (without water)20,1531
Polymers20,1531
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Membrane-extrinsic protein of photosystem II PsbP


Theoretical massNumber of molelcules
Total (without water)20,1531
Polymers20,1531
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)40.058, 38.328, 61.116
Angle α, β, γ (deg.)83.41, 66.40, 63.53
Int Tables number1
Space group name H-MP1
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B

NCS domain segments:

Component-ID: 0 / Ens-ID: 1 / Beg auth comp-ID: ASN / Beg label comp-ID: ASN / End auth comp-ID: ALA / End label comp-ID: ALA / Refine code: 0 / Auth seq-ID: 15 - 186 / Label seq-ID: 15 - 186

Dom-IDAuth asym-IDLabel asym-ID
1AA
2BB

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Components

#1: Protein Membrane-extrinsic protein of photosystem II PsbP /


Mass: 20153.379 Da / Num. of mol.: 2 / Fragment: UNP residues 73-258 / Source method: isolated from a natural source / Source: (natural) Zea mays (maize) / References: UniProt: A0A096Q0E5
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 266 / 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: 1.9 Å3/Da / Density % sol: 35.39 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 7
Details: 0.2M tri-Ammonium Citate PH7.0, 20% w/v PEG 3350, VAPOR DIFFUSION, SITTING DROP, temperature 291K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: AR-NW12A / Wavelength: 1.26 Å
DetectorType: ADSC QUANTUM 210r / Detector: CCD / Date: Dec 2, 2013
RadiationMonochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.26 Å / Relative weight: 1
ReflectionResolution: 1.6→50 Å / Num. all: 39272 / Num. obs: 37230 / % possible obs: 94.8 % / Observed criterion σ(F): 1.5 / Observed criterion σ(I): 1.5 / Redundancy: 3.9 % / Rmerge(I) obs: 0.03 / Net I/σ(I): 44.3
Reflection shellResolution: 1.6→1.63 Å / Rmerge(I) obs: 0.131 / % possible all: 90.5

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Processing

Software
NameVersionClassification
ADSCQuantumdata collection
PHASESphasing
REFMAC5.8.0073refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1V2B

1v2b


Resolution: 1.6→32.09 Å / Cor.coef. Fo:Fc: 0.958 / Cor.coef. Fo:Fc free: 0.944 / SU B: 1.438 / SU ML: 0.052 / Cross valid method: THROUGHOUT / σ(F): 1 / ESU R: 0.096 / ESU R Free: 0.09 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.19294 1860 5 %RANDOM
Rwork0.16974 ---
all0.171 37230 --
obs0.17086 35331 94.79 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 16.087 Å2
Baniso -1Baniso -2Baniso -3
1-0.01 Å2-0.04 Å20.01 Å2
2--0.03 Å2-0.01 Å2
3----0.06 Å2
Refinement stepCycle: LAST / Resolution: 1.6→32.09 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2559 0 0 266 2825
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.022607
X-RAY DIFFRACTIONr_bond_other_d0.0060.022446
X-RAY DIFFRACTIONr_angle_refined_deg1.2161.9553524
X-RAY DIFFRACTIONr_angle_other_deg0.97335653
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.3595329
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.2425.13115
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.45915440
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.4781510
X-RAY DIFFRACTIONr_chiral_restr0.0710.2389
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.022971
X-RAY DIFFRACTIONr_gen_planes_other0.0040.02575
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_it1.4771.4371328
X-RAY DIFFRACTIONr_mcbond_other1.4731.4361327
X-RAY DIFFRACTIONr_mcangle_it2.532.1411653
X-RAY DIFFRACTIONr_mcangle_other2.532.1421654
X-RAY DIFFRACTIONr_scbond_it1.8591.6461279
X-RAY DIFFRACTIONr_scbond_other1.8591.6471280
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other3.0162.3751872
X-RAY DIFFRACTIONr_long_range_B_refined5.27212.7543052
X-RAY DIFFRACTIONr_long_range_B_other5.10112.3222944
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Ens-ID: 1 / Number: 9191 / Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Rms dev position: 0.13 Å / Weight position: 0.05

Dom-IDAuth asym-ID
1A
2B
LS refinement shellResolution: 1.6→1.641 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.225 135 -
Rwork0.198 2473 -
obs--90.62 %

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