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- PDB-4uw9: The crystal structural of archaeal beta-phosphoglucomutase from h... -

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Basic information

Entry
Database: PDB / ID: 4uw9
TitleThe crystal structural of archaeal beta-phosphoglucomutase from hyper-thermophilic Pyrococcus sp. Strain ST 04
ComponentsBETA-PHOSPHOGLUCOMUTASE
KeywordsISOMERASE / ARCHAEAL PHOSPHOGLUCOMUTASE
Function / homology
Function and homology information


beta-phosphoglucomutase activity / carbohydrate metabolic process / magnesium ion binding
Similarity search - Function
Beta-phosphoglucomutase / Haloacid dehalogenase-like hydrolase / Putative phosphatase; domain 2 / Phosphoglycolate phosphatase-like, domain 2 / HAD superfamily/HAD-like / haloacid dehalogenase-like hydrolase / HAD superfamily / HAD-like superfamily / DNA polymerase; domain 1 / Rossmann fold ...Beta-phosphoglucomutase / Haloacid dehalogenase-like hydrolase / Putative phosphatase; domain 2 / Phosphoglycolate phosphatase-like, domain 2 / HAD superfamily/HAD-like / haloacid dehalogenase-like hydrolase / HAD superfamily / HAD-like superfamily / DNA polymerase; domain 1 / Rossmann fold / Orthogonal Bundle / 3-Layer(aba) Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
Beta-phosphoglucomutase
Similarity search - Component
Biological speciesPYROCOCCUS SP. ST04 (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.3 Å
AuthorsPark, K.-H. / Woo, E.-J.
CitationJournal: To be Published
Title: Structural Features of Archaeal Beta-Phosphoglucomutase from Hyper-Thermophilic Pyrococcus Sp. Strain St 04
Authors: Park, K.-H. / Jung, J.-H. / Park, C.-S. / Woo, E.-J.
History
DepositionAug 9, 2014Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 29, 2014Provider: repository / Type: Initial release
Revision 1.1Sep 23, 2015Group: Data collection
Revision 1.2Nov 13, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_entry_details / pdbx_modification_feature / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _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_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 / _struct_conn.ptnr2_label_seq_id / _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: BETA-PHOSPHOGLUCOMUTASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,0162
Polymers25,9911
Non-polymers241
Water1,54986
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)94.628, 94.628, 83.124
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number80
Space group name H-MI41

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Components

#1: Protein BETA-PHOSPHOGLUCOMUTASE


Mass: 25991.385 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) PYROCOCCUS SP. ST04 (archaea) / Production host: ESCHERICHIA COLI (E. coli) / References: UniProt: I3RFR5
#2: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 86 / 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

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Sample preparation

CrystalDensity Matthews: 3.59 Å3/Da / Density % sol: 65.7 % / Description: NONE

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Data collection

DiffractionMean temperature: 95 K
Diffraction sourceSource: SYNCHROTRON / Site: PAL/PLS / Beamline: 7A (6B, 6C1) / Wavelength: 1
DetectorType: ADSC CCD / Detector: CCD
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.3→31.22 Å / Num. obs: 16290 / % possible obs: 99 % / Observed criterion σ(I): 6.6 / Redundancy: 6 % / Rmerge(I) obs: 0.07 / Net I/σ(I): 43.67

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Processing

SoftwareName: PHENIX / Version: (PHENIX.REFINE: 1.8.4_1496) / Classification: refinement
RefinementMethod to determine structure: SAD
Starting model: NONE

Resolution: 2.3→31.225 Å / SU ML: 0.24 / σ(F): 1.17 / Phase error: 22.12 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2385 1618 9.9 %
Rwork0.1844 --
obs0.1898 16290 99.65 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.3→31.225 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1820 0 1 86 1907
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0131853
X-RAY DIFFRACTIONf_angle_d1.4082488
X-RAY DIFFRACTIONf_dihedral_angle_d15.505693
X-RAY DIFFRACTIONf_chiral_restr0.053274
X-RAY DIFFRACTIONf_plane_restr0.005315
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.3-2.36770.27331300.22231209X-RAY DIFFRACTION100
2.3677-2.44410.25471380.21321222X-RAY DIFFRACTION100
2.4441-2.53140.26751330.1931217X-RAY DIFFRACTION100
2.5314-2.63270.24971350.2031242X-RAY DIFFRACTION100
2.6327-2.75250.2211330.18991179X-RAY DIFFRACTION100
2.7525-2.89750.27071330.19731227X-RAY DIFFRACTION100
2.8975-3.07890.25051370.20541227X-RAY DIFFRACTION100
3.0789-3.31630.25051340.19971227X-RAY DIFFRACTION100
3.3163-3.64960.25481370.19261220X-RAY DIFFRACTION100
3.6496-4.17670.2121370.17881238X-RAY DIFFRACTION100
4.1767-5.25810.24751360.15321243X-RAY DIFFRACTION100
5.2581-31.22830.20231350.17451221X-RAY DIFFRACTION98

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