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- PDB-3ocz: Structure of Recombinant Haemophilus influenzae e(P4) Acid Phosph... -

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Basic information

Entry
Database: PDB / ID: 3ocz
TitleStructure of Recombinant Haemophilus influenzae e(P4) Acid Phosphatase Complexed with the inhibitor adenosine 5-O-thiomonophosphate
ComponentsLipoprotein E
KeywordsHydrolase/Hydrolase Inhibitor / hydrolase / outer membrane / Hydrolase-Hydrolase Inhibitor complex
Function / homology
Function and homology information


cell outer membrane
Similarity search - Function
5-nucleotidase lipoprotein e(P4) / Acid phosphatase, class B-like / HAD superfamily, subfamily IIIB (Acid phosphatase) / HAD superfamily/HAD-like / HAD superfamily / HAD-like superfamily / Prokaryotic membrane lipoprotein lipid attachment site profile. / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
ADENOSINE -5'-THIO-MONOPHOSPHATE / Lipoprotein E
Similarity search - Component
Biological speciesHaemophilus influenzae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.35 Å
AuthorsSingh, H. / Schuermann, J. / Reilly, T. / Calcutt, M. / Tanner, J.
CitationJournal: Febs J. / Year: 2011
Title: Structural basis of the inhibition of class C acid phosphatases by adenosine 5'-phosphorothioate.
Authors: Singh, H. / Reilly, T.J. / Tanner, J.J.
History
DepositionAug 10, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 20, 2011Provider: repository / Type: Initial release
Revision 1.1Sep 28, 2011Group: Database references
Revision 1.2Jan 11, 2012Group: Database references
Revision 1.3Nov 8, 2017Group: Advisory / Refinement description / Category: pdbx_unobs_or_zero_occ_atoms / software
Revision 1.4Sep 6, 2023Group: Advisory / Data collection ...Advisory / 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 / pdbx_unobs_or_zero_occ_atoms / 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_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: Lipoprotein E
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,0093
Polymers29,6211
Non-polymers3882
Water5,495305
1
A: Lipoprotein E
hetero molecules

A: Lipoprotein E
hetero molecules


Theoretical massNumber of molelcules
Total (without water)60,0176
Polymers59,2422
Non-polymers7754
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation8_555x-y,-y,-z1
Buried area8390 Å2
ΔGint-62 kcal/mol
Surface area18510 Å2
MethodPISA
Unit cell
Length a, b, c (Å)98.179, 98.179, 107.020
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number179
Space group name H-MP6522
Components on special symmetry positions
IDModelComponents
11A-272-

HOH

21A-565-

HOH

31A-566-

HOH

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Components

#1: Protein Lipoprotein E / Outer membrane protein P4 / OMP P4


Mass: 29620.982 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: periplasmic / Source: (gene. exp.) Haemophilus influenzae (bacteria) / Gene: hel, HI_0693, ompP4 / Plasmid: pEt20b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21DE3 / References: UniProt: P26093, acid phosphatase
#2: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#3: Chemical ChemComp-SRA / ADENOSINE -5'-THIO-MONOPHOSPHATE


Type: RNA linking / Mass: 363.287 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H14N5O6PS
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 305 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsG30E SEQUENCE CONFLICT IN UNP ENTRY P26093

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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: 2.51 Å3/Da / Density % sol: 51.06 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7
Details: 18-23 % (w/v) PEG 3350, 0.05-0.2 M ammonium citrate dibasic, 0.05-0.15 mM MgCl2, pH 7.0, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 0.9792 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Feb 26, 2010
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 1.35→50 Å / Num. obs: 67160 / % possible obs: 100 % / Redundancy: 8.2 % / Rmerge(I) obs: 0.072 / Χ2: 1.109 / Net I/σ(I): 7.8
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
1.35-1.47.90.60766030.905199.9
1.4-1.4580.47865990.9021100
1.45-1.528.10.33666160.9241100
1.52-1.68.20.26266290.9441100
1.6-1.78.30.18666540.9841100
1.7-1.838.30.13666511.0331100
1.83-2.028.30.167151.2541100
2.02-2.318.30.08467381.81100
2.31-2.918.10.05268241.3461100
2.91-5080.0371310.973199.7

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
PHENIX1.6.2_432refinement
PDB_EXTRACT3.1data extraction
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 3et4

3et4


Resolution: 1.35→33.286 Å / Occupancy max: 1 / Occupancy min: 0 / FOM work R set: 0.9294 / SU ML: 0.13 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1585 3454 5.15 %
Rwork0.1381 --
obs0.1391 67093 99.93 %
Solvent computationShrinkage radii: 0.95 Å / VDW probe radii: 1.2 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 35.145 Å2 / ksol: 0.363 e/Å3
Displacement parametersBiso max: 52.74 Å2 / Biso mean: 14.7201 Å2 / Biso min: 5.4 Å2
Baniso -1Baniso -2Baniso -3
1--1.5597 Å2-0 Å20 Å2
2---1.5597 Å2-0 Å2
3---3.1194 Å2
Refinement stepCycle: LAST / Resolution: 1.35→33.286 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1914 0 24 305 2243
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0062009
X-RAY DIFFRACTIONf_angle_d1.0812725
X-RAY DIFFRACTIONf_chiral_restr0.08275
X-RAY DIFFRACTIONf_plane_restr0.005359
X-RAY DIFFRACTIONf_dihedral_angle_d13.41736
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 25

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.35-1.36790.25211530.22182469262299
1.3679-1.38740.22411270.193624992626100
1.3874-1.40820.20411390.172925112650100
1.4082-1.43020.18191340.153524872621100
1.4302-1.45360.17961490.141825212670100
1.4536-1.47870.16521410.127724972638100
1.4787-1.50560.16821390.121525062645100
1.5056-1.53450.17671300.116125302660100
1.5345-1.56580.16311290.112825002629100
1.5658-1.59990.14851400.104125282668100
1.5999-1.63710.1391380.096525242662100
1.6371-1.6780.12581250.101425152640100
1.678-1.72340.14071380.099525362674100
1.7234-1.77410.12761620.102725082670100
1.7741-1.83140.13991260.107525252651100
1.8314-1.89680.1391440.109825512695100
1.8968-1.97280.14461570.120125012658100
1.9728-2.06250.15071400.127125472687100
2.0625-2.17130.15261290.132925752704100
2.1713-2.30730.15351240.130625782702100
2.3073-2.48540.15191350.133625752710100
2.4854-2.73540.14541370.151526022739100
2.7354-3.13090.16071240.162926112735100
3.1309-3.94360.17041620.15226332795100
3.9436-33.29640.16611320.16162810294299

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