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- PDB-1wzc: Crystal structure of Pyrococcus horikoshii mannosyl-3-phosphoglyc... -

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Basic information

Entry
Database: PDB / ID: 1wzc
TitleCrystal structure of Pyrococcus horikoshii mannosyl-3-phosphoglycerate phosphatase complexed with MG2+ and phosphate
ComponentsMannosyl-3-phosphoglycerate phosphatase
KeywordsHYDROLASE / haloacid dehalogenase like hydrolase / phosphatase
Function / homology
Function and homology information


mannosyl-3-phosphoglycerate phosphatase / mannosyl-3-phosphoglycerate phosphatase activity / mannosylglycerate biosynthetic process / magnesium ion binding / cytosol
Similarity search - Function
Mannosyl-3-phosphoglycerate phosphatase / Mannosyl-3-phosphoglycerate phosphatase, thermophiles / Putative mannosyl-3-phosphoglycerate phosphatase; domain 2 / HAD-superfamily hydrolase, superfamily IIB, MPGP / Threonyl-tRNA Synthetase; Chain A, domain 2 / HAD-superfamily hydrolase, subfamily IIB / haloacid dehalogenase-like hydrolase / HAD superfamily/HAD-like / HAD superfamily / HAD-like superfamily ...Mannosyl-3-phosphoglycerate phosphatase / Mannosyl-3-phosphoglycerate phosphatase, thermophiles / Putative mannosyl-3-phosphoglycerate phosphatase; domain 2 / HAD-superfamily hydrolase, superfamily IIB, MPGP / Threonyl-tRNA Synthetase; Chain A, domain 2 / HAD-superfamily hydrolase, subfamily IIB / haloacid dehalogenase-like hydrolase / HAD superfamily/HAD-like / HAD superfamily / HAD-like superfamily / Rossmann fold / 2-Layer Sandwich / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
PHOSPHATE ION / Mannosyl-3-phosphoglycerate phosphatase
Similarity search - Component
Biological speciesPyrococcus horikoshii (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.9 Å
AuthorsKawamura, T. / Watanabe, N. / Tanaka, I.
CitationJournal: Acta Crystallogr.,Sect.D / Year: 2008
Title: Structure of mannosyl-3-phosphoglycerate phosphatase from Pyrococcus horikoshii.
Authors: Kawamura, T. / Watanabe, N. / Tanaka, I.
History
DepositionMar 4, 2005Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Feb 28, 2006Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Mar 6, 2013Group: Other
Revision 1.4Nov 10, 2021Group: Database references / Derived calculations
Category: database_2 / pdbx_struct_conn_angle ...database_2 / pdbx_struct_conn_angle / struct_conn / 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 / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_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_asym_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_label_seq_id / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.5May 29, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Mannosyl-3-phosphoglycerate phosphatase
B: Mannosyl-3-phosphoglycerate phosphatase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)57,9416
Polymers57,7022
Non-polymers2394
Water1,838102
1
A: Mannosyl-3-phosphoglycerate phosphatase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,9703
Polymers28,8511
Non-polymers1192
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Mannosyl-3-phosphoglycerate phosphatase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,9703
Polymers28,8511
Non-polymers1192
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)59.833, 70.691, 67.911
Angle α, β, γ (deg.)90.00, 98.15, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Mannosyl-3-phosphoglycerate phosphatase / MPGP


Mass: 28851.035 Da / Num. of mol.: 2 / Mutation: A218V
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pyrococcus horikoshii (archaea) / Gene: PH0926 / Plasmid: pET-26b / Production host: Escherichia coli (E. coli)
References: UniProt: O58690, mannosyl-3-phosphoglycerate phosphatase
#2: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#3: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: PO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 102 / 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: 2

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Sample preparation

CrystalDensity Matthews: 2.53 Å3/Da / Density % sol: 51.02 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6
Details: PEG 3350, ammonium chloride, tris(hydroxymethyl)aminomethane, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
21001
Diffraction source
SourceSiteBeamlineIDWavelength (Å)
SYNCHROTRONPhoton Factory BL-5A10.9640, 0.9791, 0.9793
SYNCHROTRONPhoton Factory BL-6A21
Detector
TypeIDDetectorDateDetails
ADSC QUANTUM 3151CCDMar 20, 2004mirrors
ADSC QUANTUM 42CCDNov 6, 2004mirror
Radiation
IDMonochromatorProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1Si 111MADMx-ray1
2Si 111SINGLE WAVELENGTHMx-ray1
Radiation wavelength
IDWavelength (Å)Relative weight
10.9641
20.97911
30.97931
411
ReflectionResolution: 1.9→50 Å / Num. obs: 44446 / % possible obs: 99.9 % / Observed criterion σ(I): 0 / Redundancy: 3.8 % / Biso Wilson estimate: 28.7 Å2 / Rsym value: 0.047
Reflection shellResolution: 1.9→1.97 Å / Redundancy: 3.7 % / Mean I/σ(I) obs: 4.06 / Num. unique all: 4421 / Rsym value: 0.4 / % possible all: 100

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Processing

Software
NameClassification
DENZOdata reduction
SCALEPACKdata scaling
SHELXDphasing
SHARPphasing
RESOLVEmodel building
CNSrefinement
RESOLVEphasing
RefinementMethod to determine structure: MAD / Resolution: 1.9→50 Å / Isotropic thermal model: isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.2527 2227 -random
Rwork0.2193 ---
all-44282 --
obs-44238 94.9 %-
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--6.166 Å20 Å26.9 Å2
2--8.795 Å20 Å2
3----2.629 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.31 Å0.26 Å
Luzzati d res low-5 Å
Luzzati sigma a0.33 Å0.25 Å
Refinement stepCycle: LAST / Resolution: 1.9→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3896 0 12 102 4010
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.009204
X-RAY DIFFRACTIONc_angle_deg1.4943
X-RAY DIFFRACTIONc_dihedral_angle_d23.31802
X-RAY DIFFRACTIONc_improper_angle_d0.89783
LS refinement shellResolution: 1.9→1.97 Å
RfactorNum. reflection% reflection
Rfree0.3125 203 -
Rwork0.3734 --
obs-4398 100 %

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