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- PDB-5gne: Crystal structure of LapB from Legionella pneumophila -

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Basic information

Entry
Database: PDB / ID: 5gne
TitleCrystal structure of LapB from Legionella pneumophila
ComponentsLeucine aminopeptidase
KeywordsHYDROLASE / Aminopeptidase / Legionella pneumophila / PA domain / autoinhibition
Function / homologyPeptidase M28 family / metalloexopeptidase activity / Peptidase M28 / Peptidase family M28 / aminopeptidase activity / proteolysis / metal ion binding / Leucine aminopeptidase
Function and homology information
Biological speciesLegionella pneumophila (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 Å
AuthorsZhang, N. / Ge, H.
Funding support China, 2items
OrganizationGrant numberCountry
the National Natural Science Foundation of China31270770 China
the National Natural Science Foundation of China31400641 China
CitationJournal: J. Agric. Food Chem. / Year: 2017
Title: Crystal Structure and Biochemical Characterization of an Aminopeptidase LapB from Legionella pneumophila.
Authors: Zhang, N. / Yin, S. / Zhang, W. / Gong, X. / Zhang, N. / Fang, K. / Ge, H.
History
DepositionJul 20, 2016Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Aug 30, 2017Provider: repository / Type: Initial release
Revision 1.1Dec 6, 2017Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.2Oct 17, 2018Group: Data collection / Category: reflns / reflns_shell
Item: _reflns.pdbx_Rpim_I_all / _reflns_shell.pdbx_Rpim_I_all
Revision 1.3Nov 8, 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 / refine_hist / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _refine_hist.d_res_low / _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
Revision 1.4Oct 9, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Leucine aminopeptidase
B: Leucine aminopeptidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)84,9608
Polymers84,5072
Non-polymers4546
Water82946
1
A: Leucine aminopeptidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)42,4804
Polymers42,2531
Non-polymers2273
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Leucine aminopeptidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)42,4804
Polymers42,2531
Non-polymers2273
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)152.970, 152.970, 108.410
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number94
Space group name H-MP42212

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Components

#1: Protein Leucine aminopeptidase


Mass: 42253.312 Da / Num. of mol.: 2 / Fragment: UNP RESIDUES 24-397
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Legionella pneumophila (bacteria) / Strain: Philadelphia 1 / ATCC 33152 / DSM 7513 / Gene: lpg0032 / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta / References: UniProt: Q5ZZH8
#2: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Zn
#3: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 46 / 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: 3.75 Å3/Da / Density % sol: 67.22 %
Crystal growTemperature: 285 K / Method: vapor diffusion, hanging drop / pH: 6
Details: 0.1 M Sodium citrate tribasic dihydrate pH 6.0, 0.32 M Ammonium sulfate, 1.0 M Lithium sulfate monohydrate

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 0.97931 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Oct 25, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97931 Å / Relative weight: 1
ReflectionResolution: 2.5→48 Å / Num. obs: 42854 / % possible obs: 95.1 % / Redundancy: 17.4 % / CC1/2: 0.999 / Rmerge(I) obs: 0.108 / Rpim(I) all: 0.04 / Net I/σ(I): 18.9
Reflection shellResolution: 2.5→2.59 Å / Redundancy: 17.8 % / Rmerge(I) obs: 0.627 / Mean I/σ(I) obs: 3 / Num. unique obs: 4641 / CC1/2: 0.837 / Rpim(I) all: 0.425 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX1.8.4_1496refinement
MOSFLMdata reduction
MOSFLMdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1AMP

1amp


Resolution: 2.5→48 Å / SU ML: 0.29 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 22.98 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.227 2121 4.96 %RANDOM
Rwork0.18 ---
obs0.1826 42787 95.13 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.5→48 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5838 0 14 46 5898
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.015982
X-RAY DIFFRACTIONf_angle_d1.418114
X-RAY DIFFRACTIONf_dihedral_angle_d15.3932186
X-RAY DIFFRACTIONf_chiral_restr0.066905
X-RAY DIFFRACTIONf_plane_restr0.0071048
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.5-2.55820.32021540.25552764X-RAY DIFFRACTION100
2.5582-2.62210.27881610.23522783X-RAY DIFFRACTION100
2.6221-2.6930.32581090.24481966X-RAY DIFFRACTION70
2.693-2.77230.28071330.22082828X-RAY DIFFRACTION100
2.7723-2.86170.2921640.22772785X-RAY DIFFRACTION100
2.8617-2.9640.24031350.21462838X-RAY DIFFRACTION100
2.964-3.08270.27991540.22012811X-RAY DIFFRACTION100
3.0827-3.22290.24841560.21042811X-RAY DIFFRACTION100
3.2229-3.39280.27851490.21562847X-RAY DIFFRACTION100
3.3928-3.60530.24361280.20122335X-RAY DIFFRACTION82
3.6053-3.88360.21191140.17752461X-RAY DIFFRACTION86
3.8836-4.27420.21781420.14922536X-RAY DIFFRACTION88
4.2742-4.89220.15871270.13542899X-RAY DIFFRACTION100
4.8922-6.16170.20191450.16052932X-RAY DIFFRACTION100
6.1617-48.46960.19331500.16033070X-RAY DIFFRACTION99
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)
15.50460.27-0.892.02430.38272.5717-0.111-0.17260.21470.279-0.1637-0.05970.1370.14080.1430.26180.0351-0.01260.34140.06270.471310.7402-7.9143-23.6518
21.45670.43311.75550.85752.29856.3891-0.4059-0.05160.1292-0.9784-0.13290.0212-0.2499-0.0770.51030.37970.09650.15030.4138-0.01230.416-3.6216-23.8942-52.6111
31.82710.79751.07661.66131.54254.22430.0407-0.2833-0.0394-0.0352-0.2722-0.06690.2742-0.59390.14710.3028-0.02490.16290.29640.03220.4172-0.3983-26.2048-38.5621
43.6328-1.33050.23863.19820.18053.3482-0.02160.29210.1055-0.0816-0.0928-0.19010.33610.63420.06770.22990.15830.0290.7020.38090.526140.9079-13.1314-43.299
52.4708-1.5481.25742.3569-0.89551.2406-0.395-0.36590.21690.56630.3013-0.11870.03840.1587-0.04610.46250.1880.03330.77230.23430.545643.1586-21.8673-22.8524
62.1415-0.94180.3331.7513-0.36522.5975-0.2932-0.5531-0.24120.58820.50270.34250.0698-0.4607-0.2860.62740.54270.10411.11560.56540.548439.6922-29.5659-19.0555
72.68762.23561.06793.49051.10817.3903-0.30890.02050.6430.26220.0867-0.3758-0.72410.69790.20710.82640.2862-0.24070.96210.00530.704756.8681-18.0661-17.8075
83.41370.97132.22351.074-0.4315.2302-0.29290.17250.64730.21520.214-0.0313-0.74580.25740.1010.8040.3514-0.20820.80410.1020.680349.6512-16.0444-20.7077
91.2228-1.07362.4790.9922-2.04295.4031-0.21580.11480.44350.14910.1088-0.9027-0.47781.04310.13810.56060.2499-0.06261.04390.1210.634958.8152-27.8921-31.7305
104.2077-1.89460.89746.22170.00254.3431-0.4078-0.47870.3281.04890.4737-0.1895-0.3774-0.1991-0.04950.88240.5484-0.16510.94030.08040.492553.2418-25.5145-10.4218
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 28 through 104 )
2X-RAY DIFFRACTION2chain 'A' and (resid 105 through 132 )
3X-RAY DIFFRACTION3chain 'A' and (resid 133 through 397 )
4X-RAY DIFFRACTION4chain 'B' and (resid 28 through 77 )
5X-RAY DIFFRACTION5chain 'B' and (resid 78 through 153 )
6X-RAY DIFFRACTION6chain 'B' and (resid 154 through 286 )
7X-RAY DIFFRACTION7chain 'B' and (resid 287 through 322 )
8X-RAY DIFFRACTION8chain 'B' and (resid 323 through 356 )
9X-RAY DIFFRACTION9chain 'B' and (resid 357 through 376 )
10X-RAY DIFFRACTION10chain 'B' and (resid 377 through 397 )

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