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- PDB-6cfv: Structure of Human alpha-Phosphomannomutase 1 in complex with Ino... -

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Basic information

Entry
Database: PDB / ID: 6cfv
TitleStructure of Human alpha-Phosphomannomutase 1 in complex with Inosine Monophosphate
ComponentsPhosphomannomutase 1
KeywordsISOMERASE / phosphatase / haloalkanoate dehalogenase superfamily / mutase
Function / homology
Function and homology information


Synthesis of GDP-mannose / phosphomannomutase / phosphomannomutase activity / GDP-mannose biosynthetic process / mannose metabolic process / protein N-linked glycosylation / cellular response to leukemia inhibitory factor / neuronal cell body / metal ion binding / cytosol
Similarity search - Function
Eukaryotic phosphomannomutase, cap domain / Phosphomannomutase / Phosphomannomutase, cap domain / Eukaryotic phosphomannomutase / Hypothetical Protein, Haloacid Dehalogenase-like Hydrolase; Chain: A; domain 2 / HAD-superfamily hydrolase, subfamily IIB / HAD superfamily/HAD-like / HAD superfamily / HAD-like superfamily / Rossmann fold ...Eukaryotic phosphomannomutase, cap domain / Phosphomannomutase / Phosphomannomutase, cap domain / Eukaryotic phosphomannomutase / Hypothetical Protein, Haloacid Dehalogenase-like Hydrolase; Chain: A; domain 2 / HAD-superfamily hydrolase, subfamily IIB / HAD superfamily/HAD-like / HAD superfamily / HAD-like superfamily / Rossmann fold / 2-Layer Sandwich / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
INOSINIC ACID / Phosphomannomutase 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.918 Å
AuthorsJi, T. / Dunaway-Mariano, D. / Allen, K.N.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM103403 United States
CitationJournal: Biochemistry / Year: 2018
Title: Structural Basis of the Molecular Switch between Phosphatase and Mutase Functions of Human Phosphomannomutase 1 under Ischemic Conditions.
Authors: Ji, T. / Zhang, C. / Zheng, L. / Dunaway-Mariano, D. / Allen, K.N.
History
DepositionFeb 17, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 9, 2018Provider: repository / Type: Initial release
Revision 1.1May 23, 2018Group: Data collection / Database references / Category: citation / Item: _citation.title
Revision 1.2Jul 4, 2018Group: Data collection / Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.3Nov 27, 2019Group: Author supporting evidence / Category: pdbx_audit_support
Item: _pdbx_audit_support.funding_organization / _pdbx_audit_support.grant_number
Revision 1.4Oct 4, 2023Group: Advisory / Data collection ...Advisory / Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / pdbx_unobs_or_zero_occ_atoms / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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.ptnr2_symmetry / _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 / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _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_symmetry

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Phosphomannomutase 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,1844
Polymers29,7871
Non-polymers3973
Water5,170287
1


  • Idetical with deposited unit
  • defined by software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)52.169, 52.169, 214.484
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212
Components on special symmetry positions
IDModelComponents
11A-450-

HOH

21A-585-

HOH

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Components

#1: Protein Phosphomannomutase 1 / / PMM 1 / PMMH-22


Mass: 29786.811 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PMM1, PMMH22 / Production host: Escherichia coli (E. coli) / References: UniProt: Q92871, phosphomannomutase
#2: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#3: Chemical ChemComp-IMP / INOSINIC ACID / Inosinic acid


Mass: 348.206 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H13N4O8P
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 287 / 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: 2.45 Å3/Da / Density % sol: 49.79 %
Crystal growTemperature: 290 K / Method: vapor diffusion, hanging drop
Details: 20% polyethylene glycol 3350, 0.15 M DL-malate, pH 7.0, 50 mM MgCl2, and 8 mM beta-mercaptoethanol

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL12-2 / Wavelength: 0.97917 Å
DetectorType: MARMOSAIC 325 mm CCD / Detector: CCD / Date: Apr 26, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97917 Å / Relative weight: 1
ReflectionResolution: 1.918→34.88 Å / Num. obs: 23377 / % possible obs: 98.2 % / Redundancy: 2 % / Net I/σ(I): 30.32
Reflection shellResolution: 1.918→1.966 Å

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Processing

Software
NameVersionClassification
PHENIX1.8.2_1309refinement
XDSdata reduction
XDSdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2FUC
Resolution: 1.918→34.88 Å / SU ML: 0.19 / Cross valid method: FREE R-VALUE / σ(F): 0 / Phase error: 20.64
RfactorNum. reflection% reflection
Rfree0.2256 1970 8.57 %
Rwork0.1723 --
obs0.1766 23000 96.64 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.918→34.88 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1966 0 25 287 2278
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0072034
X-RAY DIFFRACTIONf_angle_d1.0122741
X-RAY DIFFRACTIONf_dihedral_angle_d13.65771
X-RAY DIFFRACTIONf_chiral_restr0.077293
X-RAY DIFFRACTIONf_plane_restr0.005359
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.9178-1.96570.26171020.19991099X-RAY DIFFRACTION73
1.9657-2.01890.22291330.19251434X-RAY DIFFRACTION94
2.0189-2.07830.23461390.17221476X-RAY DIFFRACTION98
2.0783-2.14530.25861380.17441458X-RAY DIFFRACTION97
2.1453-2.2220.22511390.16881495X-RAY DIFFRACTION98
2.222-2.3110.22631400.17431514X-RAY DIFFRACTION99
2.311-2.41610.24091430.18441508X-RAY DIFFRACTION98
2.4161-2.54350.26291440.1811521X-RAY DIFFRACTION99
2.5435-2.70270.22841440.1821532X-RAY DIFFRACTION99
2.7027-2.91130.23171460.19271560X-RAY DIFFRACTION99
2.9113-3.20410.19841450.17991544X-RAY DIFFRACTION100
3.2041-3.66730.22311460.17181566X-RAY DIFFRACTION99
3.6673-4.61880.1971510.14471612X-RAY DIFFRACTION100
4.6188-34.88880.23991600.17281711X-RAY DIFFRACTION99

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