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- PDB-2cu2: Crystal structure of mannose-1-phosphate geranyltransferase from ... -

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Basic information

Entry
Database: PDB / ID: 2cu2
TitleCrystal structure of mannose-1-phosphate geranyltransferase from Thermus thermophilus HB8
Componentsputative mannose-1-phosphate guanylyl transferase
KeywordsTRANSFERASE / mannose-1-phosphate geranyltransferase / Thermus thermophilus HB8 / Structural Genomics / RIKEN Structural Genomics/Proteomics Initiative / RSGI / NPPSFA / National Project on Protein Structural and Functional Analyses
Function / homology
Function and homology information


mannose-1-phosphate guanylyltransferase (GTP) activity / GDP-mannose biosynthetic process / isomerase activity
Similarity search - Function
: / : / : / MannoseP isomerase/GMP-like beta-helix domain / Nucleotidyl transferase domain / Nucleotidyl transferase / Spore Coat Polysaccharide Biosynthesis Protein SpsA; Chain A / Spore Coat Polysaccharide Biosynthesis Protein SpsA; Chain A / Nucleotide-diphospho-sugar transferases / Alpha-Beta Complex / Alpha Beta
Similarity search - Domain/homology
Mannose-1-phosphate guanylyl transferase (GDP)/mannose-6-phosphate isomerase
Similarity search - Component
Biological speciesThermus thermophilus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.2 Å
AuthorsSugahara, M. / Kunishima, N. / RIKEN Structural Genomics/Proteomics Initiative (RSGI)
CitationJournal: To be Published
Title: Crystal structure of mannose-1-phosphate geranyltransferase from Thermus thermophilus HB8
Authors: Sugahara, M. / Kunishima, N.
History
DepositionMay 25, 2005Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Aug 8, 2006Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Source and taxonomy / Version format compliance
Revision 1.3Mar 13, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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: putative mannose-1-phosphate guanylyl transferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,6803
Polymers37,4881
Non-polymers1922
Water4,197233
1
A: putative mannose-1-phosphate guanylyl transferase
hetero molecules

A: putative mannose-1-phosphate guanylyl transferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)75,3606
Polymers74,9762
Non-polymers3844
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_656-x+1,y,-z+11
Unit cell
Length a, b, c (Å)84.128, 91.185, 118.633
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number23
Space group name H-MI222
Components on special symmetry positions
IDModelComponents
11A-1164-

HOH

21A-1220-

HOH

DetailsThe biological assembly is a dimer in the asymmetric unit by the operations: -x+1, y, -z+1.

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Components

#1: Protein putative mannose-1-phosphate guanylyl transferase / mannose-1-phosphate geranyltransferase


Mass: 37487.867 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermus thermophilus (bacteria) / Strain: HB8 / Plasmid: pET11a / Production host: Escherichia coli (E. coli)
References: UniProt: Q5SHI0, mannose-1-phosphate guanylyltransferase
#2: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 233 / 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: 3.1 Å3/Da / Density % sol: 59.7 %
Crystal growTemperature: 295 K / Method: microbatch / pH: 8.5
Details: lithium sulphate, pH 8.5, microbatch , temperature 295K

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
21001
Diffraction source
SourceSiteBeamlineIDWavelength (Å)
SYNCHROTRONSPring-8 BL26B111
SYNCHROTRONSPring-8 BL26B120.97904
Detector
TypeIDDetectorDate
RIGAKU RAXIS IV1IMAGE PLATEOct 5, 2004
RIGAKU RAXIS IV2IMAGE PLATEMay 15, 2005
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
111
20.979041
ReflectionResolution: 2.2→40 Å / Num. all: 23487 / Num. obs: 23487 / % possible obs: 99.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 8 % / Biso Wilson estimate: 39.749 Å2 / Rmerge(I) obs: 0.07 / Rsym value: 0.066 / Net I/σ(I): 10.1
Reflection shellResolution: 2.2→2.28 Å / Redundancy: 8.1 % / Rmerge(I) obs: 0.62 / Mean I/σ(I) obs: 3.8 / Num. unique all: 2307 / Rsym value: 0.58 / % possible all: 100

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Processing

Software
NameVersionClassification
HKL-2000data collection
SCALEPACKdata scaling
SOLVEphasing
CNS1.1refinement
HKL-2000data reduction
RefinementMethod to determine structure: SAD / Resolution: 2.2→37.98 Å / Isotropic thermal model: Anisotrop / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.253 1176 -RANDOM
Rwork0.219 ---
all0.219 23487 --
obs0.219 23487 99.8 %-
Displacement parametersBiso mean: 41.1 Å2
Baniso -1Baniso -2Baniso -3
1--2.83 Å20 Å20 Å2
2--4.29 Å20 Å2
3----1.46 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.33 Å0.28 Å
Luzzati d res low-5 Å
Luzzati sigma a0.24 Å0.22 Å
Refinement stepCycle: LAST / Resolution: 2.2→37.98 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2627 0 10 233 2870
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_angle_deg0.013
X-RAY DIFFRACTIONc_bond_d1.7
LS refinement shellResolution: 2.2→2.28 Å / Rfactor Rfree error: 0.028
RfactorNum. reflection% reflection
Rfree0.275 97 -
Rwork0.258 --
obs-2185 99 %

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