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- PDB-3n1u: Structure of putative HAD superfamily (subfamily III A) hydrolase... -

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Basic information

Entry
Database: PDB / ID: 3n1u
TitleStructure of putative HAD superfamily (subfamily III A) hydrolase from Legionella pneumophila
ComponentsHydrolase, HAD superfamily, subfamily III A
KeywordsHYDROLASE / structural genomics / PSI-2 / Protein Structure Initiative / New York SGX Research Center for Structural Genomics / NYSGXRC
Function / homology
Function and homology information


3-deoxy-manno-octulosonate-8-phosphatase activity / 3-deoxy-manno-octulosonate-8-phosphatase / lipopolysaccharide biosynthetic process / metal ion binding
Similarity search - Function
KdsC family / : / HAD-superfamily hydrolase,subfamily IIIA / haloacid dehalogenase-like hydrolase / HAD superfamily/HAD-like / HAD superfamily / HAD-like superfamily / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
3-deoxy-D-manno-octulosonate 8-phosphate phosphatase KdsC
Similarity search - Component
Biological speciesLegionella pneumophila (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.8 Å
AuthorsRamagopal, U.A. / Toro, R. / Burley, S.K. / Almo, S.C. / New York SGX Research Center for Structural Genomics (NYSGXRC)
CitationJournal: To be published
Title: Structure of putative HAD superfamily (subfamily III A) hydrolase from Legionella pneumophila
Authors: Ramagopal, U.A. / Toro, R. / Burley, S.K. / Almo, S.C.
History
DepositionMay 17, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 21, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 8, 2017Group: Refinement description / Category: software
Revision 1.3Feb 10, 2021Group: Database references / Derived calculations / Structure summary
Category: audit_author / citation_author ...audit_author / citation_author / pdbx_struct_conn_angle / struct_conn / struct_ref_seq_dif / struct_site
Item: _audit_author.identifier_ORCID / _citation_author.identifier_ORCID ..._audit_author.identifier_ORCID / _citation_author.identifier_ORCID / _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_seq_id / _pdbx_struct_conn_angle.ptnr2_label_alt_id / _pdbx_struct_conn_angle.ptnr2_label_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.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_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
Revision 1.4Oct 16, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Hydrolase, HAD superfamily, subfamily III A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,5373
Polymers21,4571
Non-polymers802
Water1,31573
1
A: Hydrolase, HAD superfamily, subfamily III A
hetero molecules

A: Hydrolase, HAD superfamily, subfamily III A
hetero molecules

A: Hydrolase, HAD superfamily, subfamily III A
hetero molecules

A: Hydrolase, HAD superfamily, subfamily III A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)86,14712
Polymers85,8274
Non-polymers3218
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,-y,z1
crystal symmetry operation3_555-y,x,z1
crystal symmetry operation4_555y,-x,z1
Buried area9270 Å2
ΔGint-103 kcal/mol
Surface area28770 Å2
MethodPISA
Unit cell
Length a, b, c (Å)80.907, 80.907, 65.295
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number79
Space group name H-MI4

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Components

#1: Protein Hydrolase, HAD superfamily, subfamily III A


Mass: 21456.682 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Legionella pneumophila (bacteria) / Strain: subsp. pneumophila str. Philadelphia 1 / Gene: lpg0839 / Plasmid: BC-pSGX4(BC) / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q5ZX93
#2: Chemical ChemComp-CA / CALCIUM ION


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


Mass: 18.015 Da / Num. of mol.: 73 / Source method: isolated from a natural source / Formula: H2O
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: 2.49 Å3/Da / Density % sol: 50.6 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 0.1M Sodium Cacodylate pH 6.5, 18% PEG 8k, 0.1M Calcium Acetate, Vapor diffusion, Sitting drop, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X29A / Wavelength: 0.9793 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Mar 28, 2010
RadiationProtocol: SINGLE WAVELENGTH / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9793 Å / Relative weight: 1
ReflectionResolution: 1.8→50 Å / Num. obs: 19515 / % possible obs: 99.6 % / Redundancy: 11.7 % / Rmerge(I) obs: 0.073 / Χ2: 1.432 / Net I/σ(I): 16.9
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2% possible all
1.8-1.836.50.3429471.0197.1
1.83-1.8680.2949501.06499.3
1.86-1.910.60.3089651.047100
1.9-1.9412.10.25310071.095100
1.94-1.9812.50.229561.123100
1.98-2.0312.60.2129631.21100
2.03-2.0812.50.1679901.282100
2.08-2.1312.50.1389841.364100
2.13-2.212.50.1259671.432100
2.2-2.2712.60.1139971.511100
2.27-2.3512.50.1019531.445100
2.35-2.4412.60.0969911.5100
2.44-2.5512.50.0899581.509100
2.55-2.6912.50.0829841.551100
2.69-2.8612.40.0789921.644100
2.86-3.0812.40.0699691.61100
3.08-3.3912.20.0699891.53899.9
3.39-3.8811.90.0679911.53999.4
3.88-4.8811.40.0599691.6198.8
4.88-5011.30.0619932.19697

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
REFMACrefinement
PDB_EXTRACT3.1data extraction
CBASSdata collection
HKL-2000data reduction
HKL2Mapphasing
CCP4phasing
RefinementMethod to determine structure: SAD / Resolution: 1.8→50 Å / Cor.coef. Fo:Fc: 0.967 / Cor.coef. Fo:Fc free: 0.952 / WRfactor Rfree: 0.23 / WRfactor Rwork: 0.189 / Occupancy max: 1 / Occupancy min: 0.5 / FOM work R set: 0.837 / SU B: 6.108 / SU ML: 0.084 / SU R Cruickshank DPI: 0.112 / SU Rfree: 0.114 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.114 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : RESIDUAL ONLY
RfactorNum. reflection% reflectionSelection details
Rfree0.217 997 5.1 %RANDOM
Rwork0.176 ---
obs0.178 19495 99.34 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso max: 54.97 Å2 / Biso mean: 37.016 Å2 / Biso min: 13.41 Å2
Baniso -1Baniso -2Baniso -3
1--1.31 Å20 Å20 Å2
2---1.31 Å20 Å2
3---2.63 Å2
Refinement stepCycle: LAST / Resolution: 1.8→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1406 0 2 73 1481
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.020.0221449
X-RAY DIFFRACTIONr_angle_refined_deg1.5741.9681961
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.2775187
X-RAY DIFFRACTIONr_dihedral_angle_2_deg40.65525.79769
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.01215269
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.109157
X-RAY DIFFRACTIONr_chiral_restr0.1330.2227
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.021082
X-RAY DIFFRACTIONr_mcbond_it1.0121.5908
X-RAY DIFFRACTIONr_mcangle_it1.68221455
X-RAY DIFFRACTIONr_scbond_it2.8463541
X-RAY DIFFRACTIONr_scangle_it4.6164.5504
LS refinement shellResolution: 1.799→1.845 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.331 69 -
Rwork0.266 1296 -
all-1365 -
obs--95.86 %
Refinement TLS params.Method: refined / Origin x: 21.541 Å / Origin y: 2.127 Å / Origin z: 1.419 Å
111213212223313233
T0.0072 Å2-0.0016 Å20.0122 Å2-0.0458 Å2-0.0342 Å2--0.2204 Å2
L2.8061 °20.3984 °20.6141 °2-1.1613 °20.0948 °2--0.9092 °2
S0.0664 Å °0.0265 Å °0.0674 Å °-0.0034 Å °0.0092 Å °-0.178 Å °-0.025 Å °0.1546 Å °-0.0756 Å °

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