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- PDB-5k8k: Structure of the Haemophilus influenzae LpxH-lipid X complex -

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Basic information

Entry
Database: PDB / ID: 5k8k
TitleStructure of the Haemophilus influenzae LpxH-lipid X complex
ComponentsUDP-2,3-diacylglucosamine hydrolase
KeywordsHYDROLASE / LpxH / lipid X / UDP-diacylglucosamine / lipid A / LPS / lipopolysaccharide / antibiotic / calcineurin-like phosphoesterase
Function / homology
Function and homology information


UDP-2,3-diacylglucosamine diphosphatase / UDP-2,3-diacylglucosamine hydrolase activity / lipid A biosynthetic process / extrinsic component of plasma membrane / manganese ion binding / cytoplasm
Similarity search - Function
UDP-2,3-diacylglucosamine hydrolase / UDP-2,3-diacylglucosamine hydrolase LpxH-like / Calcineurin-like phosphoesterase domain, ApaH type / Calcineurin-like phosphoesterase / Metallo-dependent phosphatase-like
Similarity search - Domain/homology
ACETATE ION / Chem-LP5 / : / UDP-2,3-diacylglucosamine hydrolase
Similarity search - Component
Biological speciesHaemophilus influenzae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.55 Å
AuthorsCho, J. / Lee, C.-J. / Zhou, P.
Funding support United States, 2items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM115355 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM51310 United States
CitationJournal: Nat Microbiol / Year: 2016
Title: Structure of the essential Haemophilus influenzae UDP-diacylglucosamine pyrophosphohydrolase LpxH in lipid A biosynthesis.
Authors: Cho, J. / Lee, C.J. / Zhao, J. / Young, H.E. / Zhou, P.
History
DepositionMay 30, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 10, 2016Provider: repository / Type: Initial release
Revision 1.1Sep 21, 2016Group: Database references
Revision 1.2Nov 9, 2016Group: Database references
Revision 1.3Sep 20, 2017Group: Author supporting evidence / Derived calculations / Category: pdbx_audit_support / pdbx_struct_oper_list
Item: _pdbx_audit_support.funding_organization / _pdbx_struct_oper_list.symmetry_operation
Revision 1.4Dec 25, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.5Oct 23, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.pdbx_ptnr1_label_alt_id / _struct_conn.pdbx_ptnr2_label_alt_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_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
Remark 650 HELIX DETERMINATION METHOD: AUTHOR DETERMINED
Remark 700 SHEET DETERMINATION METHOD: AUTHOR DETERMINED

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: UDP-2,3-diacylglucosamine hydrolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,6408
Polymers30,5161
Non-polymers1,1247
Water34219
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)99.840, 99.840, 200.850
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number155
Space group name H-MH32

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Components

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Protein , 1 types, 1 molecules A

#1: Protein UDP-2,3-diacylglucosamine hydrolase / UDP-2 / 3-diacylglucosamine diphosphatase


Mass: 30515.965 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Haemophilus influenzae (strain ATCC 51907 / DSM 11121 / KW20 / Rd) (bacteria)
Strain: ATCC 51907 / DSM 11121 / KW20 / Rd / Gene: lpxH, HI_0735 / Production host: Escherichia coli (E. coli)
References: UniProt: P44046, UDP-2,3-diacylglucosamine diphosphatase

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Non-polymers , 5 types, 26 molecules

#2: Chemical ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mn
#3: Chemical ChemComp-LP5 / (R)-((2R,3S,4R,5R,6R)-3-HYDROXY-2-(HYDROXYMETHYL)-5-((R)-3-HYDROXYTETRADECANAMIDO)-6-(PHOSPHONOOXY)TETRAHYDRO-2H-PYRAN-4-YL) 3-HYDROXYTETRADECANOATE


Mass: 711.861 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C34H66NO12P
#4: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H3O2
#5: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 19 / Source method: isolated from a natural source / Formula: H2O

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Details

Has protein modificationY

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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: 3.44 Å3/Da / Density % sol: 64.23 %
Crystal growTemperature: 288 K / Method: vapor diffusion, sitting drop
Details: 100 mM NaCl, 10 mM HEPES, 35 mM sodium acetate pH 4.1, 2.2% PEG 4000, 0.3 mM sulfonyl piperazine, 0.7% DMSO, 22% glycerol, and ~3-4 mM n-decyl-beta-D-thiomaltopyranoside.
Temp details: 4.1

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Nov 28, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.55→79.42 Å / Num. obs: 12876 / % possible obs: 100 % / Observed criterion σ(I): -3 / Biso Wilson estimate: 51.07 Å2 / Rmerge(I) obs: 0.052 / Net I/σ(I): 27.59
Reflection shellResolution: 2.55→2.62 Å / Rmerge(I) obs: 0.739 / Mean I/σ(I) obs: 4.36 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX1.10.1_2155refinement
Aimless0.1.27data scaling
XSCALEVERSION Oct 15, 2015data scaling
PDB_EXTRACT3.2data extraction
XDSOct 15, 2015data reduction
PHENIX1.10.1-2155phasing
RefinementMethod to determine structure: SAD / Resolution: 2.55→79.42 Å / SU ML: 0.29 / Cross valid method: FREE R-VALUE / σ(F): 1.37 / Phase error: 21.98 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.227 1278 9.93 %
Rwork0.192 --
obs0.195 12872 99.9 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 58.77 Å2
Refinement stepCycle: LAST / Resolution: 2.55→79.42 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1869 0 70 19 1958
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0042031
X-RAY DIFFRACTIONf_angle_d0.6172732
X-RAY DIFFRACTIONf_dihedral_angle_d11.1231196
X-RAY DIFFRACTIONf_chiral_restr0.042301
X-RAY DIFFRACTIONf_plane_restr0.004346
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.55-2.65210.29851500.27111237X-RAY DIFFRACTION100
2.6521-2.77280.29351520.22831279X-RAY DIFFRACTION100
2.7728-2.9190.24441340.22041271X-RAY DIFFRACTION100
2.919-3.10190.26981550.20581258X-RAY DIFFRACTION100
3.1019-3.34140.23731460.19361276X-RAY DIFFRACTION100
3.3414-3.67770.20841280.17421293X-RAY DIFFRACTION100
3.6777-4.20980.21951420.17681290X-RAY DIFFRACTION100
4.2098-5.30380.21421390.16351304X-RAY DIFFRACTION100
5.3038-79.45620.20151320.20761386X-RAY DIFFRACTION100
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°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)
12.1862-0.54620.7752.2918-0.41683.9126-0.3205-0.49720.25140.67260.2604-0.1405-0.04820.20.05010.45620.15520.00330.4218-0.06340.3587-8.358433.524818.3413
20.4047-0.4487-0.16680.9692-0.30612.5894-0.1445-0.0801-0.36230.1190.2699-0.18681.20750.6808-0.08870.8510.39450.02250.57360.02250.5815-1.432914.549314.5872
34.1649-2.1575-0.34152.5840.12530.3074-0.09060.6040.3641-0.2277-0.0087-0.88810.31780.9050.05950.38270.150.10450.6435-0.0090.4916-2.788928.7967-2.474
42.240.9691-0.65972.06691.34822.137-0.13840.34290.2974-0.12410.1254-0.5715-0.33440.8682-0.04870.2849-0.05450.05220.43650.01270.5592-2.323638.23464.2064
50.3138-0.4225-0.52742.3987-0.3561.6515-0.11140.05430.3835-0.04480.15020.0432-0.68870.3765-0.02390.6185-0.0212-0.05920.4363-0.04710.696-4.902546.958112.0585
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1CHAIN 'A' AND (RESID 1 THROUGH 123 )
2X-RAY DIFFRACTION2CHAIN 'A' AND (RESID 124 THROUGH 166 )
3X-RAY DIFFRACTION3CHAIN 'A' AND (RESID 167 THROUGH 187 )
4X-RAY DIFFRACTION4CHAIN 'A' AND (RESID 188 THROUGH 217 )
5X-RAY DIFFRACTION5CHAIN 'A' AND (RESID 218 THROUGH 237 )

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