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- PDB-4lq6: Crystal structure of Rv3717 reveals a novel amidase from M. tuber... -

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Basic information

Entry
Database: PDB / ID: 4lq6
TitleCrystal structure of Rv3717 reveals a novel amidase from M. tuberculosis
ComponentsN-acetymuramyl-L-alanine amidase-related protein
KeywordsHYDROLASE / Amidase / cell wall hydrolase
Function / homology
Function and homology information


N-acetylmuramoyl-L-alanine amidase activity / peptidoglycan catabolic process / metal ion binding
Similarity search - Function
Zn-dependent exopeptidases / : / Ami_3 / N-acetylmuramoyl-L-alanine amidase, catalytic domain / N-acetylmuramoyl-L-alanine amidase / Aminopeptidase / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
: / N-acetymuramyl-L-alanine amidase-related protein
Similarity search - Component
Biological speciesMycobacterium tuberculosis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.68 Å
AuthorsKumar, A. / Kumar, S. / Kumar, D. / Mishra, A. / Dewangan, R.P. / Shrivastava, P. / Ramachandran, S. / Taneja, B.
CitationJournal: Acta Crystallogr.,Sect.D / Year: 2013
Title: The structure of Rv3717 reveals a novel amidase from Mycobacterium tuberculosis.
Authors: Kumar, A. / Kumar, S. / Kumar, D. / Mishra, A. / Dewangan, R.P. / Shrivastava, P. / Ramachandran, S. / Taneja, B.
History
DepositionJul 17, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 4, 2013Provider: repository / Type: Initial release
Revision 1.1Jan 15, 2014Group: Database references
Revision 1.2Nov 6, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / 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_alt_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.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_alt_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_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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: N-acetymuramyl-L-alanine amidase-related protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,58510
Polymers22,6961
Non-polymers8899
Water3,441191
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)37.350, 103.780, 129.970
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number24
Space group name H-MI212121
Components on special symmetry positions
IDModelComponents
11A-582-

HOH

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Components

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Protein , 1 types, 1 molecules A

#1: Protein N-acetymuramyl-L-alanine amidase-related protein


Mass: 22696.316 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium tuberculosis (bacteria) / Gene: MT3820, Rv3717 / Production host: Escherichia coli (E. coli) / References: UniProt: O69684

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Non-polymers , 5 types, 200 molecules

#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#3: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#4: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Cl
#5: Chemical ChemComp-PT / PLATINUM (II) ION


Mass: 195.078 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Pt
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 191 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 2.77 Å3/Da / Density % sol: 55.67 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: Ammonium sulfate, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: BM14 / Wavelength: 1.0714 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: May 16, 2012
RadiationMonochromator: silicon mirrors / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0714 Å / Relative weight: 1
ReflectionResolution: 1.68→29.52 Å / Num. all: 29381 / Num. obs: 29381 / % possible obs: 100 % / Observed criterion σ(F): 3 / Observed criterion σ(I): 0 / Biso Wilson estimate: 21.46 Å2
Reflection shellResolution: 1.68→1.74 Å / % possible all: 3.23

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Processing

Software
NameVersionClassification
HKL-2000data collection
Auto-Rickshawphasing
BUSTER2.10.0refinement
MOSFLMdata reduction
SCALAdata scaling
RefinementMethod to determine structure: SAD / Resolution: 1.68→21.09 Å / Cor.coef. Fo:Fc: 0.9601 / Cor.coef. Fo:Fc free: 0.9501 / SU R Cruickshank DPI: 0.079 / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.1842 1495 5.09 %RANDOM
Rwork0.1605 ---
obs0.1617 29370 99.99 %-
all-29381 --
Displacement parametersBiso mean: 23.58 Å2
Baniso -1Baniso -2Baniso -3
1--0.0235 Å20 Å20 Å2
2---0.237 Å20 Å2
3---0.2605 Å2
Refine analyzeLuzzati coordinate error obs: 0.177 Å
Refinement stepCycle: LAST / Resolution: 1.68→21.09 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1556 0 13 191 1760
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.011661HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.032265HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d576SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes45HARMONIC2
X-RAY DIFFRACTIONt_gen_planes260HARMONIC5
X-RAY DIFFRACTIONt_it1661HARMONIC20
X-RAY DIFFRACTIONt_nbd13SEMIHARMONIC5
X-RAY DIFFRACTIONt_omega_torsion3.41
X-RAY DIFFRACTIONt_other_torsion16.32
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion209SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact2243SEMIHARMONIC4
LS refinement shellResolution: 1.68→1.74 Å / Total num. of bins used: 15
RfactorNum. reflection% reflection
Rfree0.1927 140 4.91 %
Rwork0.1696 2713 -
all0.1709 2853 -
obs--99.99 %
Refinement TLS params.Method: refined / Origin x: 10.6726 Å / Origin y: 40.9984 Å / Origin z: 45.2963 Å
111213212223313233
T-0.0491 Å2-0.0049 Å2-0.0364 Å2--0.0435 Å20.026 Å2---0.0244 Å2
L1.2034 °20.061 °2-0.0197 °2-1.1342 °20.1276 °2--0.9346 °2
S-0.0372 Å °0.079 Å °0.1692 Å °0.0299 Å °0.0349 Å °-0.0491 Å °-0.0604 Å °0.0387 Å °0.0023 Å °
Refinement TLS groupSelection details: { A|2 - 214 }

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