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- PDB-3l1u: Crystal structure of Calcium-bound GmhB from E. coli. -

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Basic information

Entry
Database: PDB / ID: 3l1u
TitleCrystal structure of Calcium-bound GmhB from E. coli.
ComponentsD,D-heptose 1,7-bisphosphate phosphatase
KeywordsHYDROLASE / LPS biosynthesis / sugar phosphatase / heptose / zinc / Carbohydrate metabolism / Cytoplasm / Lipopolysaccharide biosynthesis
Function / homology
Function and homology information


D-glycero-beta-D-manno-heptose 1,7-bisphosphate 7-phosphatase / D-glycero-beta-D-manno-heptose 1,7-bisphosphate 7-phosphatase activity / ADP-L-glycero-beta-D-manno-heptose biosynthetic process / lipopolysaccharide core region biosynthetic process / magnesium ion binding / zinc ion binding / cytosol
Similarity search - Function
D,D-heptose 1,7-bisphosphate phosphatase / Histidinol-phosphate phosphatase / HAD-superfamily hydrolase,subfamily IIIA / HAD-hyrolase-like / HAD superfamily/HAD-like / HAD superfamily / HAD-like superfamily / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
D-glycero-beta-D-manno-heptose-1,7-bisphosphate 7-phosphatase
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.95 Å
AuthorsSugiman-Marangos, S.N. / Junop, M.S.
CitationJournal: Biochemistry / Year: 2010
Title: Structural and kinetic characterization of the LPS biosynthetic enzyme D-alpha,beta-D-heptose-1,7-bisphosphate phosphatase (GmhB) from Escherichia coli.
Authors: Taylor, P.L. / Sugiman-Marangos, S. / Zhang, K. / Valvano, M.A. / Wright, G.D. / Junop, M.S.
History
DepositionDec 14, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 5, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Oct 25, 2017Group: Author supporting evidence / Category: pdbx_struct_assembly_auth_evidence
Revision 1.3Sep 6, 2023Group: Data collection / Database references ...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 / 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_asym_id / _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.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_comp_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr2_label_atom_id / _pdbx_struct_conn_angle.ptnr2_label_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_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_asym_id / _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_asym_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_ref_seq_dif.details / _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

Downloads & links

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Assembly

Deposited unit
A: D,D-heptose 1,7-bisphosphate phosphatase
B: D,D-heptose 1,7-bisphosphate phosphatase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,1926
Polymers46,9812
Non-polymers2114
Water6,215345
1
A: D,D-heptose 1,7-bisphosphate phosphatase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,5963
Polymers23,4911
Non-polymers1052
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: D,D-heptose 1,7-bisphosphate phosphatase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,5963
Polymers23,4911
Non-polymers1052
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)50.553, 64.031, 105.236
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
DetailsThe biological assembly is a monomer as judged by gel filtration chromatography.

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Components

#1: Protein D,D-heptose 1,7-bisphosphate phosphatase / D-glycero-D-manno-heptose 1 / 7-bisphosphate phosphatase


Mass: 23490.607 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Strain: K-12 / Gene: b0200, gmhB, JW0196, yaeD / Plasmid: pet28b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)
References: UniProt: P63228, Hydrolases; Acting on ester bonds; Phosphoric-monoester hydrolases
#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
#3: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ca
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 345 / 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: 1.81 Å3/Da / Density % sol: 32.14 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.8
Details: 25% PEG 3350, 0.1M Tris, 0.005M DTT, 0.025M sodium chloride, 0.005M calcium chloride, 11% glycerol , pH 7.8, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU300 / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: Sep 8, 2008 / Details: mirrors
RadiationMonochromator: Blue confocal optics mirrors / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.95→45.59 Å / Num. all: 25327 / Num. obs: 25327 / % possible obs: 99 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Redundancy: 4.03 % / Biso Wilson estimate: 26.1 Å2 / Rmerge(I) obs: 0.062 / Net I/σ(I): 9.2
Reflection shellResolution: 1.95→2.02 Å / Redundancy: 3.91 % / Rmerge(I) obs: 0.331 / Mean I/σ(I) obs: 3.4 / Num. unique all: 2517 / % possible all: 98.8

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Processing

Software
NameVersionClassification
CrystalCleardata collection
PHENIXmodel building
PHENIX(phenix.refine: 1.5_2)refinement
CrystalCleardata reduction
CrystalCleardata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2GMW

2gmw


Resolution: 1.95→45.568 Å / SU ML: 0.25 / Isotropic thermal model: isotropic / Cross valid method: THROUGHOUT / σ(F): 0.06 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2578 1965 7.9 %Random
Rwork0.235 ---
all0.2385 25327 --
obs0.2367 24872 96.91 %-
Solvent computationShrinkage radii: 0.8 Å / VDW probe radii: 1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 40.31 Å2 / ksol: 0.37 e/Å3
Displacement parametersBiso mean: 29.93 Å2
Refinement stepCycle: LAST / Resolution: 1.95→45.568 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2857 0 4 345 3206
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0062921
X-RAY DIFFRACTIONf_angle_d1.0123966
X-RAY DIFFRACTIONf_dihedral_angle_d18.7761060
X-RAY DIFFRACTIONf_chiral_restr0.052438
X-RAY DIFFRACTIONf_plane_restr0.003521
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.95-1.99660.36371320.35671516X-RAY DIFFRACTION92
1.9966-2.05060.36051360.31621608X-RAY DIFFRACTION97
2.0506-2.1110.33121390.26711626X-RAY DIFFRACTION98
2.111-2.17910.26611430.26321644X-RAY DIFFRACTION99
2.1791-2.2570.26771430.25451651X-RAY DIFFRACTION99
2.257-2.34730.291410.25171627X-RAY DIFFRACTION99
2.3473-2.45420.24271410.23781660X-RAY DIFFRACTION99
2.4542-2.58350.2691410.24171658X-RAY DIFFRACTION99
2.5835-2.74540.30681430.24841653X-RAY DIFFRACTION98
2.7454-2.95730.25871400.26251660X-RAY DIFFRACTION98
2.9573-3.25480.24631420.2291656X-RAY DIFFRACTION97
3.2548-3.72560.23271420.19121651X-RAY DIFFRACTION97
3.7256-4.69320.19291410.18121654X-RAY DIFFRACTION96
4.6932-45.58040.21391410.2151643X-RAY DIFFRACTION90

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