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- PDB-3et5: Structure of Recombinant Haemophilus Influenzae E(P4) Acid Phosph... -

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Basic information

Entry
Database: PDB / ID: 3et5
TitleStructure of Recombinant Haemophilus Influenzae E(P4) Acid Phosphatase Complexed with tungstate
ComponentsOuter membrane protein P4, NADP phosphatase
KeywordsHYDROLASE / haloacid dehalogenase (had) fold / dddd motif / class c nonspecific acid phosphatase
Function / homology
Function and homology information


cell outer membrane / metal ion binding
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
TUNGSTATE(VI)ION / Outer membrane protein P4, NADP phosphatase
Similarity search - Component
Biological speciesHaemophilus influenzae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 2 Å
AuthorsTanner, J.J.
CitationJournal: Biochemistry / Year: 2007
Title: Structure of Recombinant Haemophilus Influenzae E (P4) Acid Phosphatase Reveals a New Member of the Haloacid Dehalogenase Superfamily.
Authors: Felts, R.L. / Ou, Z. / Reilly, T.J. / Tanner, J.J.
History
DepositionOct 6, 2008Deposition site: RCSB / Processing site: RCSB
SupersessionOct 14, 2008ID: 2HLL
Revision 1.0Oct 14, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2Dec 27, 2023Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / 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_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.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.value / _struct_conn.pdbx_dist_value / _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

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Assembly

Deposited unit
A: Outer membrane protein P4, NADP phosphatase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,0744
Polymers28,6081
Non-polymers4663
Water2,558142
1
A: Outer membrane protein P4, NADP phosphatase
hetero molecules

A: Outer membrane protein P4, NADP phosphatase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)58,1498
Polymers57,2162
Non-polymers9336
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_655-x+1,-y,z1
Buried area7710 Å2
ΔGint-53 kcal/mol
Surface area18690 Å2
MethodPISA
Unit cell
Length a, b, c (Å)65.848, 65.848, 101.893
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number94
Space group name H-MP42212
Components on special symmetry positions
IDModelComponents
11A-351-

HOH

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Components

#1: Protein Outer membrane protein P4, NADP phosphatase / recombinant e(P4) acid phosphatase


Mass: 28608.002 Da / Num. of mol.: 1 / Fragment: UNP residues 22-274
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Haemophilus influenzae (bacteria) / Strain: 86-028NP / Gene: hel, NTHI0816 / Production host: Escherichia coli (E. coli) / References: UniProt: Q4QMM5, 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-WO4 / TUNGSTATE(VI)ION


Mass: 247.838 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: WO4
#4: Chemical ChemComp-PG4 / TETRAETHYLENE GLYCOL / Polyethylene glycol


Mass: 194.226 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H18O5 / Comment: precipitant*YM
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 142 / 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: 1.93 Å3/Da / Density % sol: 36.24 %
Crystal growpH: 8.5
Details: 40% PEG 4000, 0.1 M TRIS-HCL, 0.2 M MAGNESIUM CHLORIDE, PH 8.5, VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 295K, pH 8.50

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Data collection

DiffractionMean temperature: 173 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 4.2.2 / Wavelength: 1.0052
DetectorType: NOIR-1 / Detector: CCD / Date: Aug 28, 2005
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0052 Å / Relative weight: 1
ReflectionResolution: 2→46.56 Å / Num. obs: 15761 / % possible obs: 99.7 % / Observed criterion σ(I): 0 / Redundancy: 7.07 % / Rmerge(I) obs: 0.117 / Net I/σ(I): 9.1
Reflection shellResolution: 2→2.07 Å / Redundancy: 7.13 % / Rmerge(I) obs: 0.416 / Mean I/σ(I) obs: 3.8 / % possible all: 100

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Processing

Software
NameVersionClassification
SOLVEphasing
REFMAC5.2.0005refinement
d*TREKdata reduction
d*TREKdata scaling
RefinementMethod to determine structure: FOURIER SYNTHESIS / Resolution: 2→42.3 Å / Cor.coef. Fo:Fc: 0.953 / Cor.coef. Fo:Fc free: 0.933 / SU B: 7.435 / SU ML: 0.125 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.209 / ESU R Free: 0.171 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.225 783 5 %RANDOM
Rwork0.182 ---
obs0.185 15737 99.7 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 19.21 Å2
Baniso -1Baniso -2Baniso -3
1--0.32 Å20 Å20 Å2
2---0.32 Å20 Å2
3---0.63 Å2
Refinement stepCycle: LAST / Resolution: 2→42.3 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1916 0 13 142 2071
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0221991
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.3131.9272678
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.9615247
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.03525.238105
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.74115336
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.1159
X-RAY DIFFRACTIONr_chiral_restr0.0930.2270
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.021549
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2040.2851
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3030.21331
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1260.2138
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1740.280
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.190.225
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.5971.51240
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it0.89521907
X-RAY DIFFRACTIONr_scbond_it1.6353877
X-RAY DIFFRACTIONr_scangle_it2.3754.5769
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2→2.05 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.282 59 -
Rwork0.22 1066 -
obs--100 %
Refinement TLS params.Method: refined / Origin x: 21.366 Å / Origin y: 4.58 Å / Origin z: 20.654 Å
111213212223313233
T-0.0998 Å20.0292 Å20.0326 Å2--0.1233 Å20.0152 Å2---0.0772 Å2
L2.1481 °2-0.2297 °2-0.2434 °2-2.2975 °20.0841 °2--0.8434 °2
S0.1123 Å °0.28 Å °0.1081 Å °0.0911 Å °-0.102 Å °0.3573 Å °-0.025 Å °-0.1492 Å °-0.0103 Å °

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