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- PDB-3l1v: Crystal structure of GmhB from E. coli in complex with calcium an... -

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Basic information

Entry
Database: PDB / ID: 3l1v
TitleCrystal structure of GmhB from E. coli in complex with calcium and phosphate.
ComponentsD,D-heptose 1,7-bisphosphate phosphatase
KeywordsHYDROLASE / LPS biosynthesis / Sugar phosphatase / Zinc / heptose / 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
PHOSPHATE ION / 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: 1.954 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)47,3828
Polymers46,9812
Non-polymers4016
Water4,522251
1
A: D,D-heptose 1,7-bisphosphate phosphatase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,6914
Polymers23,4911
Non-polymers2003
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)23,6914
Polymers23,4911
Non-polymers2003
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)50.575, 64.309, 104.381
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
DetailsThe biological assembly of GmhB 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: Chemical ChemComp-PO4 / PHOSPHATE ION


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


Mass: 18.015 Da / Num. of mol.: 251 / 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: 31.91 %
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, 0.005M sodium phosphate, 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 5, 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→45.29 Å / Num. all: 24747 / Num. obs: 24747 / % possible obs: 98.3 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Redundancy: 3.89 % / Biso Wilson estimate: 31.8 Å2 / Rmerge(I) obs: 0.11 / Net I/σ(I): 6.6
Reflection shellResolution: 1.95→2.02 Å / Redundancy: 3.89 % / Rmerge(I) obs: 0.426 / Mean I/σ(I) obs: 2.6 / Num. unique all: 2468 / % possible all: 100

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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: 1.954→27.135 Å / SU ML: 0.33 / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / σ(F): 0.02 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2838 1928 8.08 %RANDOM
Rwork0.2464 ---
all0.253 24747 --
obs0.2494 23855 94.14 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.2 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 37.107 Å2 / ksol: 0.385 e/Å3
Displacement parametersBiso mean: 32.84 Å2
Refinement stepCycle: LAST / Resolution: 1.954→27.135 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2830 0 14 251 3095
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0142900
X-RAY DIFFRACTIONf_angle_d1.363942
X-RAY DIFFRACTIONf_dihedral_angle_d18.3311034
X-RAY DIFFRACTIONf_chiral_restr0.115436
X-RAY DIFFRACTIONf_plane_restr0.007518
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.954-2.02390.41421810.37762094X-RAY DIFFRACTION92
2.0239-2.1050.34831970.35692250X-RAY DIFFRACTION98
2.105-2.20070.33452010.30932248X-RAY DIFFRACTION98
2.2007-2.31670.35191950.28532219X-RAY DIFFRACTION97
2.3167-2.46170.2861960.25852235X-RAY DIFFRACTION97
2.4617-2.65170.29911950.26682199X-RAY DIFFRACTION95
2.6517-2.91820.2861920.26122194X-RAY DIFFRACTION94
2.9182-3.33990.25431930.23372172X-RAY DIFFRACTION93
3.3399-4.20530.24161870.1832111X-RAY DIFFRACTION89
4.2053-27.13730.23621910.19242205X-RAY DIFFRACTION89
Refinement TLS params.

Refine-ID: X-RAY DIFFRACTION

IDMethodL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
1refined1.1414-0.2351-0.91611.1449-0.29970.7390.1002-0.09870.0134-0.06610.0987-0.0057-0.05710.21810.01880.2068-0.006-0.05360.16260.0240.091814.817.5365-23.2611
21.5536-0.69691.25770.6173-1.37394.9688-0.3838-0.2693-0.13290.17220.1308-0.05370.2644-0.44930.18440.22590.05-0.00610.19120.03610.1853
32.76450.9589-0.48730.48690.33341.8701-0.5826-0.00790.51550.17450.32690.4272-0.49790.00490.11080.30510.117-0.03180.20930.00050.2509
40.8249-0.50330.72971.1544-1.29641.6253-0.1489-0.1426-0.06210.2084-0.0351-0.1189-0.3262-0.11610.1720.33440.02540.01750.12940.00910.292
50.3105-0.0121-0.0082.66280.42011.0047-0.1643-0.7064-0.6418-0.17980.5616-0.09460.05840.0004-0.34650.1224-0.01610.02460.28060.03470.1262
63.86121.63271.32830.90530.54920.53960.22520.1129-0.3816-0.11390.0142-0.32310.39230.0321-0.22070.0843-0.0645-0.10440.06960.05570.1681
71.1792-0.2169-1.17110.916-0.08671.2748-0.5031-0.18510.0322-0.15050.1416-0.0051-0.27340.09070.2670.2541-0.0648-0.07660.17560.0170.1537
81.8972.0957-0.03085.90370.3120.1594-0.00890.1788-0.2179-0.83-0.002-0.4227-0.2651-0.070.05880.26620.02130.00960.11010.01050.0679
90.47440.69450.32371.1550.49150.258-0.0778-0.2149-0.2282-0.23570.3778-0.40970.09240.0573-0.18560.24130.03810.07410.21420.0460.4339
100.79560.1378-0.86270.0035-0.11141.1650.2201-0.1003-0.0076-0.1731-0.28830.0676-0.21890.2131-0.08790.24980.02910.06750.21020.00220.0881
111.4866-0.3824-0.67060.4279-0.21692.1381-0.122-0.0022-0.210.05670.1144-0.03930.2789-0.07860.0510.17040.0327-0.03690.07260.00160.1871
120.4713-0.1177-0.74580.26220.4660.6559-0.0379-0.1242-0.1928-0.0239-0.10410.02510.07110.17670.06040.15320.0090.01740.1916-0.03460.191
131.3351-0.9084-1.50891.51940.48822.0073-0.4085-0.46520.23880.09320.397-0.19260.4020.50440.04740.16070.1284-0.03510.2547-0.03140.1974
140.73520.493-0.19491.1225-0.76770.51230.0099-0.00950.04680.1563-0.0723-0.0818-0.14670.11680.05450.14030.0238-0.02590.1504-0.01140.1621
150.34060.0561-0.60820.14890.00532.49340.1406-0.02550.59070.2735-0.16960.2419-0.84720.4431-0.02080.4246-0.0247-0.00750.1461-0.1250.2188
161.6920.7262-0.93970.3756-0.18921.0440.1127-0.03460.2295-0.10140.0628-0.1413-0.11840.122-0.10910.18170.0329-0.05460.1185-0.05280.3076
171.7260.44511.051.35620.32854.12190.6280.3383-0.4409-0.52150.0225-0.336-0.25380.4416-0.66360.2697-0.01830.02190.2429-0.01560.3959
181.5895-0.18420.355.2387-0.57880.41320.09350.0013-0.40780.4714-0.20020.3948-0.0914-0.0455-0.04760.20320.0142-0.04810.1391-0.03840.3954
190.42440.0372-0.41222.6560.29741.14220.25-0.15260.62-0.36420.15060.9653-0.03070.0387-0.33270.1651-0.0268-0.03520.15730.00490.4287
200.984-0.1215-0.49670.11-0.13110.8338-0.19710.2731-0.4906-0.0588-0.05750.4168-0.2296-0.14010.22370.28280.0104-0.03020.1349-0.07810.2711
Refinement TLS groupSelection details: chain B and resid 184:205)

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