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- PDB-3hze: Crystal Structure of Ycf54 protein from Thermosynechococcus elong... -

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Basic information

Entry
Database: PDB / ID: 3hze
TitleCrystal Structure of Ycf54 protein from Thermosynechococcus elongatus, Northeast Structural Genomics Consortium Target TeR59
ComponentsYcf54 protein
KeywordsSTRUCTURAL GENOMICS / UNKNOWN FUNCTION / PSI-2 / Protein Structure Initiative / Northeast Structural Genomics Consortium / NESG / TeR59 / Q8DIT2_SYNEL
Function / homologyUncharacterised protein family Ycf54 / Ycf54 protein / Ycf54-like superfamily / Ycf54 protein / Alpha-Beta Plaits / 2-Layer Sandwich / Alpha Beta / PHOSPHATE ION / Ycf54 protein
Function and homology information
Biological speciesThermosynechococcus elongatus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2 Å
AuthorsKuzin, A. / Abashidze, M. / Seetharaman, J. / Sahdev, S. / Xiao, R. / Ciccosanti, C. / Lee, D. / Everett, J.K. / Nair, R. / Acton, T.B. ...Kuzin, A. / Abashidze, M. / Seetharaman, J. / Sahdev, S. / Xiao, R. / Ciccosanti, C. / Lee, D. / Everett, J.K. / Nair, R. / Acton, T.B. / Rost, B. / Montelione, G.T. / Tong, L. / Hunt, J.F. / Northeast Structural Genomics Consortium (NESG)
CitationJournal: To be Published
Title: Northeast Structural Genomics Consortium Target TeR59
Authors: Kuzin, A. / Abashidze, M. / Seetharaman, J. / Sahdev, S. / Xiao, R. / Ciccosanti, C. / Lee, D. / Everett, J.K. / Nair, R. / Acton, T.B. / Rost, B. / Montelione, G.T. / Hunt, J.F. / Tong, L.
History
DepositionJun 23, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 7, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Source and taxonomy / Version format compliance
Revision 1.2Jul 24, 2019Group: Data collection / Derived calculations / Refinement description
Category: software / struct_conn
Item: _software.contact_author / _software.contact_author_email ..._software.contact_author / _software.contact_author_email / _software.language / _software.location / _software.name / _software.type / _software.version / _struct_conn.pdbx_leaving_atom_flag
Revision 1.3Oct 30, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Ycf54 protein
B: Ycf54 protein
C: Ycf54 protein
D: Ycf54 protein
E: Ycf54 protein
F: Ycf54 protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)82,1407
Polymers82,0456
Non-polymers951
Water6,666370
1
A: Ycf54 protein


Theoretical massNumber of molelcules
Total (without water)13,6741
Polymers13,6741
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Ycf54 protein


Theoretical massNumber of molelcules
Total (without water)13,6741
Polymers13,6741
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Ycf54 protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)13,7692
Polymers13,6741
Non-polymers951
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: Ycf54 protein


Theoretical massNumber of molelcules
Total (without water)13,6741
Polymers13,6741
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
5
E: Ycf54 protein


Theoretical massNumber of molelcules
Total (without water)13,6741
Polymers13,6741
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
6
F: Ycf54 protein


Theoretical massNumber of molelcules
Total (without water)13,6741
Polymers13,6741
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)82.432, 86.075, 123.060
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein
Ycf54 protein


Mass: 13674.159 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermosynechococcus elongatus (bacteria)
Strain: BP-1 / Gene: tll1499, ycf54 / Plasmid: BL21 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)+ Magic / References: UniProt: Q8DIT2
#2: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: PO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 370 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 2.66 Å3/Da / Density % sol: 53.77 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5.6
Details: 1.26M NaH2PO4, 0.14M K2HPO4, pH 5.6, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X4A / Wavelength: 0.97853 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Jun 17, 2009
RadiationMonochromator: Si 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97853 Å / Relative weight: 1
ReflectionResolution: 1.9→50 Å / Num. all: 133729 / Num. obs: 1028186 / % possible obs: 100 % / Observed criterion σ(I): -3 / Redundancy: 7.7 % / Rmerge(I) obs: 0.084 / Net I/σ(I): 19.6
Reflection shellResolution: 1.9→1.97 Å / Redundancy: 7.6 % / Rmerge(I) obs: 0.491 / Mean I/σ(I) obs: 2.9 / Num. unique all: 13357 / % possible all: 100

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Processing

Software
NameVersionClassificationNB
CNS1.2refinement
PDB_EXTRACT3data extraction
ADSCQuantumdata collection
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing
REFMACrefinement
RefinementMethod to determine structure: SAD / Resolution: 2→20 Å / σ(F): 4209 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflection
Rfree0.232 5347 4.7 %
Rwork0.207 --
obs-107096 93.8 %
Solvent computationBsol: 52.944 Å2
Displacement parametersBiso mean: 24.171 Å2
Baniso -1Baniso -2Baniso -3
1--0.225 Å20 Å20 Å2
2---3.046 Å20 Å2
3---3.272 Å2
Refinement stepCycle: LAST / Resolution: 2→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5360 0 5 370 5735
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.006
X-RAY DIFFRACTIONc_angle_d1.263
X-RAY DIFFRACTIONc_mcbond_it1.4491.5
X-RAY DIFFRACTIONc_scbond_it2.3512
X-RAY DIFFRACTIONc_mcangle_it2.2772
X-RAY DIFFRACTIONc_scangle_it3.5282.5
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2dna-rna_rep.paramdna-rna.top
X-RAY DIFFRACTION3water_rep.paramwater.top
X-RAY DIFFRACTION4ion.paramion.top

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