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- PDB-3neh: Crystal structure of the protein LMO2462 from Listeria monocytoge... -

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Basic information

Entry
Database: PDB / ID: 3neh
TitleCrystal structure of the protein LMO2462 from Listeria monocytogenes complexed with ZN and phosphonate mimic of dipeptide L-Leu-D-Ala
ComponentsRenal dipeptidase family protein
KeywordsLYASE / Structural genomics / NYSGRC / dipeptide L-Leu-D-Ala / PSI-2 / Protein Structure Initiative / New York SGX Research Center for Structural Genomics / NYSGXRC
Function / homologyMetal-dependent hydrolases / TIM Barrel / Alpha-Beta Barrel / Alpha Beta / Chem-L3A / :
Function and homology information
Biological speciesListeria monocytogenes (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.642 Å
AuthorsFedorov, A.A. / Fedorov, E.V. / Cummings, J. / Raushel, F.M. / Burley, S.K. / Almo, S.C. / New York SGX Research Center for Structural Genomics (NYSGXRC)
CitationJournal: To be Published
Title: Crystal structure of the protein LMO2462 from Listeria monocytogenes complexed with ZN and phosphonate mimic of dipeptide L-Leu-D-Ala
Authors: Fedorov, A.A. / Fedorov, E.V. / Cummings, J. / Raushel, F.M. / Sauder, J.M. / Burley, S.K. / Almo, S.C.
History
DepositionJun 8, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 30, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Feb 10, 2021Group: Advisory / Database references ...Advisory / Database references / Derived calculations / Structure summary
Category: audit_author / citation_author ...audit_author / citation_author / pdbx_struct_conn_angle / pdbx_unobs_or_zero_occ_atoms / 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_asym_id / _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_asym_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_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.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_seq_id / _struct_conn.ptnr2_label_asym_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 1.3Sep 6, 2023Group: Advisory / Data collection ...Advisory / Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_unobs_or_zero_occ_atoms
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Renal dipeptidase family protein
B: Renal dipeptidase family protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)73,0088
Polymers72,2722
Non-polymers7366
Water6,377354
1
A: Renal dipeptidase family protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,5044
Polymers36,1361
Non-polymers3683
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Renal dipeptidase family protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,5044
Polymers36,1361
Non-polymers3683
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)53.834, 79.453, 152.014
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Renal dipeptidase family protein


Mass: 36136.039 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Listeria monocytogenes (bacteria) / Strain: 4b F2365 / Gene: LMOf2365_2435 / Production host: Escherichia coli (E. coli) / References: UniProt: Q71WW4, protoporphyrin ferrochelatase
#2: Chemical ChemComp-L3A / (2R)-3-[(R)-[(1R)-1-amino-3-methylbutyl](hydroxy)phosphoryl]-2-methylpropanoic acid / L-LEU-D-ALA PHOSPHINATE PSEUDODIPEPTIDE


Type: peptide-like / Mass: 237.233 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C9H20NO4P
#3: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Zn
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 354 / 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: 2.25 Å3/Da / Density % sol: 45.31 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 25% PEG 3350, 0.1M Bis-Tris, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 293.0K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X4A / Wavelength: 0.97915 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Mar 4, 2010
RadiationMonochromator: Si 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97915 Å / Relative weight: 1
ReflectionResolution: 1.642→39.727 Å / Num. all: 75524 / Num. obs: 75524 / % possible obs: 93.95 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Rmerge(I) obs: 0.094

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Processing

Software
NameVersionClassification
ADSCQuantumdata collection
BALBESphasing
PHENIX(phenix.refine: 1.5_2)refinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3LU2

3lu2


Resolution: 1.642→39.727 Å / SU ML: 0.21 / SU R Cruickshank DPI: 0.9 / σ(F): 0 / σ(I): 0 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2193 3802 5.03 %
Rwork0.1967 --
all0.1979 75524 -
obs0.1979 75524 93.95 %
Solvent computationIon probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 39.708 Å2 / ksol: 0.339 e/Å3
Displacement parametersBiso min: 24.17 Å2
Baniso -1Baniso -2Baniso -3
1--2.7282 Å20 Å2-0 Å2
2--5.7448 Å2-0 Å2
3----3.0166 Å2
Refinement stepCycle: LAST / Resolution: 1.642→39.727 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4928 0 34 354 5316
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0075074
X-RAY DIFFRACTIONf_angle_d1.0736854
X-RAY DIFFRACTIONf_dihedral_angle_d15.7081872
X-RAY DIFFRACTIONf_chiral_restr0.074755
X-RAY DIFFRACTIONf_plane_restr0.004885
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.6424-1.66320.3546490.33821130X-RAY DIFFRACTION40
1.6632-1.68510.3818750.32151611X-RAY DIFFRACTION57
1.6851-1.70810.362990.32791902X-RAY DIFFRACTION69
1.7081-1.73250.33171260.30222322X-RAY DIFFRACTION82
1.7325-1.75840.35771280.28592534X-RAY DIFFRACTION91
1.7584-1.78590.2921290.27452702X-RAY DIFFRACTION96
1.7859-1.81520.281390.25812787X-RAY DIFFRACTION100
1.8152-1.84650.2871330.23442811X-RAY DIFFRACTION100
1.8465-1.880.29021490.22112796X-RAY DIFFRACTION100
1.88-1.91620.24871480.21682801X-RAY DIFFRACTION100
1.9162-1.95530.25681490.20932780X-RAY DIFFRACTION100
1.9553-1.99780.23651490.20452851X-RAY DIFFRACTION100
1.9978-2.04430.24321630.19512778X-RAY DIFFRACTION100
2.0443-2.09540.20391500.18642800X-RAY DIFFRACTION100
2.0954-2.15210.22121530.18242813X-RAY DIFFRACTION100
2.1521-2.21540.19591660.1792780X-RAY DIFFRACTION100
2.2154-2.28690.21321400.18782815X-RAY DIFFRACTION100
2.2869-2.36860.23391550.18262796X-RAY DIFFRACTION100
2.3686-2.46340.20971230.18682891X-RAY DIFFRACTION100
2.4634-2.57550.21881750.18872809X-RAY DIFFRACTION100
2.5755-2.71130.21811530.19382814X-RAY DIFFRACTION100
2.7113-2.88110.24031530.21082832X-RAY DIFFRACTION100
2.8811-3.10350.24171690.20612862X-RAY DIFFRACTION100
3.1035-3.41560.20431510.20322845X-RAY DIFFRACTION100
3.4156-3.90950.20941630.17292883X-RAY DIFFRACTION100
3.9095-4.92410.17571580.15362921X-RAY DIFFRACTION100
4.9241-39.73810.18061570.19273056X-RAY DIFFRACTION100

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