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- PDB-3tb5: Crystal Structure of the Enterococcus faecalis Methionine aminope... -

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Basic information

Entry
Database: PDB / ID: 3tb5
TitleCrystal Structure of the Enterococcus faecalis Methionine aminopeptidase apo form
ComponentsMethionine aminopeptidase
KeywordsHYDROLASE / Methionine aminopeptidase / metalloprotease / enterococcus feacalis
Function / homologyCreatine Amidinohydrolase / Creatinase/methionine aminopeptidase superfamily / Alpha-Beta Complex / Alpha Beta / CITRIC ACID / :
Function and homology information
Biological speciesEnterococcus faecalis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å
AuthorsKishor, C. / Gumpena, R. / Reddi, R. / Addlagatta, A.
CitationJournal: MEDCHEMCOMM / Year: 2012
Title: Structural studies of Enterococcus faecalis methionine aminopeptidase and design of microbe specific 2,2'-bipyridine based inhibitors
Authors: Kishor, C. / Gumpena, R. / Reddi, R. / Addlagatta, A.
History
DepositionAug 5, 2011Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Aug 8, 2012Provider: repository / Type: Initial release
Revision 1.1Jun 26, 2013Group: Database references
Revision 1.2Nov 1, 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 / 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 / _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: Methionine aminopeptidase
B: Methionine aminopeptidase
C: Methionine aminopeptidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)88,7335
Polymers88,3483
Non-polymers3842
Water2,864159
1
A: Methionine aminopeptidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,6422
Polymers29,4491
Non-polymers1921
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Methionine aminopeptidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,6422
Polymers29,4491
Non-polymers1921
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: Methionine aminopeptidase


Theoretical massNumber of molelcules
Total (without water)29,4491
Polymers29,4491
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)120.740, 132.130, 85.300
Angle α, β, γ (deg.)90.00, 133.36, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein Methionine aminopeptidase


Mass: 29449.436 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Enterococcus faecalis (bacteria) / Strain: HIP11704 / Gene: EFHG_00941, MetAP / Plasmid: pET28a / Production host: Escherichia coli (E. coli) / References: UniProt: C7VIN6, methionyl aminopeptidase
#2: Chemical ChemComp-CIT / CITRIC ACID


Mass: 192.124 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H8O7
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 159 / 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: 4

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Sample preparation

CrystalDensity Matthews: 2.8 Å3/Da / Density % sol: 56.07 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 5.6
Details: 14-20% PEG 3400, 0.14M (NH4)2H-citrate, 8% glycerol, pH 5.4-6.2, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.2.2 / Wavelength: 0.9919 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Mar 25, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9919 Å / Relative weight: 1
ReflectionResolution: 2.3→45.22 Å / Num. obs: 43107 / % possible obs: 99 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.5 % / Rmerge(I) obs: 0.052 / Rsym value: 0.033

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Processing

Software
NameVersionClassification
APEXdata collection
MOLREPphasing
REFMAC5.5.0110refinement
iMOSFLMdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1C21

1c21


Resolution: 2.3→36.47 Å / Cor.coef. Fo:Fc: 0.939 / Cor.coef. Fo:Fc free: 0.895 / SU B: 5.834 / SU ML: 0.146 / Cross valid method: THROUGHOUT / ESU R: 0.269 / ESU R Free: 0.226 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.25484 2157 5 %RANDOM
Rwork0.19707 ---
obs0.19995 40925 99.92 %-
all-1397 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 37.177 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refinement stepCycle: LAST / Resolution: 2.3→36.47 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5557 0 26 159 5742
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0240.0225870
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg2.111.9747964
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.6455751
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.57824.419258
X-RAY DIFFRACTIONr_dihedral_angle_3_deg20.263151048
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.5081532
X-RAY DIFFRACTIONr_chiral_restr0.1730.2870
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.0214438
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.071.53591
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.93625818
X-RAY DIFFRACTIONr_scbond_it3.30532279
X-RAY DIFFRACTIONr_scangle_it5.274.52124
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.3→2.36 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.303 166 -
Rwork0.231 2988 -
obs--99.97 %

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