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- PDB-7ff5: The crystal structure of Ruminiclostridium cellulolyticum Phospho... -

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Basic information

Entry
Database: PDB / ID: 7ff5
TitleThe crystal structure of Ruminiclostridium cellulolyticum Phosphocarrier
ComponentsPhosphocarrier, HPr family
KeywordsSIGNALING PROTEIN / Ruminiclostridium cellulolyticum Phosphocarrier
Function / homologyPhosphotransferase system, HPr serine phosphorylation site / PTS HPR domain serine phosphorylation site signature. / Phosphocarrier protein HPr-like / HPr-like superfamily / PTS HPr component phosphorylation site / PTS HPR domain profile. / Phosphocarrier, HPr family
Function and homology information
Biological speciesRuminiclostridium cellulolyticum H10 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.37 Å
AuthorsZhang, N. / Ge, H.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC) China
CitationJournal: To Be Published
Title: The crystal structure of Ruminiclostridium cellulolyticum Phosphocarrier
Authors: Zhang, N. / Ge, H.
History
DepositionJul 22, 2021Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jul 27, 2022Provider: repository / Type: Initial release
Revision 1.1Nov 29, 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: Phosphocarrier, HPr family
B: Phosphocarrier, HPr family
C: Phosphocarrier, HPr family
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,59210
Polymers29,9203
Non-polymers6727
Water1,24369
1
A: Phosphocarrier, HPr family
hetero molecules


Theoretical massNumber of molelcules
Total (without water)10,4546
Polymers9,9731
Non-polymers4805
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area160 Å2
ΔGint-12 kcal/mol
Surface area4780 Å2
MethodPISA
2
B: Phosphocarrier, HPr family
hetero molecules


Theoretical massNumber of molelcules
Total (without water)10,0692
Polymers9,9731
Non-polymers961
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area4700 Å2
MethodPISA
3
C: Phosphocarrier, HPr family
hetero molecules


Theoretical massNumber of molelcules
Total (without water)10,0692
Polymers9,9731
Non-polymers961
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area4760 Å2
MethodPISA
Unit cell
Length a, b, c (Å)96.004, 96.004, 89.836
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number92
Space group name H-MP41212
Components on special symmetry positions
IDModelComponents
11A-238-

HOH

Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
12A
22C
13B
23C

NCS domain segments:

Component-ID: 0 / Beg auth comp-ID: MET / Beg label comp-ID: MET / End auth comp-ID: GLY / End label comp-ID: GLY / Refine code: 0 / Auth seq-ID: 1 - 84 / Label seq-ID: 1 - 84

Dom-IDEns-IDAuth asym-IDLabel asym-ID
11AA
21BB
12AA
22CC
13BB
23CC

NCS ensembles :
ID
1
2
3

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Components

#1: Protein Phosphocarrier, HPr family


Mass: 9973.345 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Ruminiclostridium cellulolyticum H10 (bacteria)
Strain: H10 / Gene: Ccel_0806 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: B8I8F1
#2: Chemical
ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: SO4 / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 69 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 3.46 Å3/Da / Density % sol: 64.44 %
Crystal growTemperature: 288 K / Method: vapor diffusion, hanging drop
Details: 0.2 M Sodium sulfate, 20% w/v PEG3350, 10% w/v Ethylene glycol

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL18U1 / Wavelength: 0.97915 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Jan 7, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97915 Å / Relative weight: 1
ReflectionResolution: 2.37→30 Å / Num. obs: 17552 / % possible obs: 99.6 % / Redundancy: 1.9 % / CC1/2: 0.999 / Rmerge(I) obs: 0.015 / Net I/σ(I): 36.4
Reflection shellResolution: 2.37→2.45 Å / Rmerge(I) obs: 0.061 / Num. unique obs: 1694 / CC1/2: 0.988

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Processing

Software
NameVersionClassification
PHENIXv1.16refinement
PDB_EXTRACT3.27data extraction
HKL-3000data reduction
SCALEPACKdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1MO1

1mo1


Resolution: 2.37→30 Å / Cor.coef. Fo:Fc: 0.942 / Cor.coef. Fo:Fc free: 0.895 / SU B: 6.137 / SU ML: 0.149 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.245 / ESU R Free: 0.213 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2562 795 4.5 %RANDOM
Rwork0.2137 ---
obs0.2156 16744 99.4 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 161.74 Å2 / Biso mean: 54.822 Å2 / Biso min: 23.89 Å2
Baniso -1Baniso -2Baniso -3
1--0.03 Å20 Å20 Å2
2---0.03 Å20 Å2
3---0.06 Å2
Refinement stepCycle: final / Resolution: 2.37→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1881 0 35 69 1985
Biso mean--72.5 46.48 -
Num. residues----252
Refine LS restraints NCS

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

Ens-IDDom-IDAuth asym-IDNumberRms dev position (Å)
11A23090.14
12B23090.14
21A22390.16
22C22390.16
31B22850.15
32C22850.15
LS refinement shellResolution: 2.37→2.43 Å / Rfactor Rfree error: 0
RfactorNum. reflection% reflection
Rfree0.268 51 -
Rwork0.23 1192 -
obs--96.43 %

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