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- PDB-1rjm: Crystal Structure of MenB (Rv0548c) from Mycobacterium tuberculosis -

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Basic information

Entry
Database: PDB / ID: 1rjm
TitleCrystal Structure of MenB (Rv0548c) from Mycobacterium tuberculosis
ComponentsMenBNaphthoate synthase
KeywordsLYASE / Crotonase-like family / beta-beta-alpha / Structural Genomics / PSI / Protein Structure Initiative / TB Structural Genomics Consortium / TBSGC
Function / homology
Function and homology information


1,4-dihydroxy-2-naphthoyl-CoA synthase / 1,4-dihydroxy-2-naphthoyl-CoA synthase activity / menaquinone biosynthetic process / protein hexamerization / plasma membrane
Similarity search - Function
1,4-Dihydroxy-2-naphthoyl-CoA synthase, MenB / Lyase 2-enoyl-coa Hydratase, Chain A, domain 2 / Lyase 2-enoyl-coa Hydratase; Chain A, domain 2 / Enoyl-CoA hydratase, C-terminal / Enoyl-CoA hydratase/isomerase / Enoyl-CoA hydratase/isomerase / 2-enoyl-CoA Hydratase; Chain A, domain 1 / 2-enoyl-CoA Hydratase; Chain A, domain 1 / ClpP/crotonase-like domain superfamily / Alpha-Beta Complex ...1,4-Dihydroxy-2-naphthoyl-CoA synthase, MenB / Lyase 2-enoyl-coa Hydratase, Chain A, domain 2 / Lyase 2-enoyl-coa Hydratase; Chain A, domain 2 / Enoyl-CoA hydratase, C-terminal / Enoyl-CoA hydratase/isomerase / Enoyl-CoA hydratase/isomerase / 2-enoyl-CoA Hydratase; Chain A, domain 1 / 2-enoyl-CoA Hydratase; Chain A, domain 1 / ClpP/crotonase-like domain superfamily / Alpha-Beta Complex / Orthogonal Bundle / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
Chem-EP1 / 1,4-dihydroxy-2-naphthoyl-CoA synthase / 1,4-dihydroxy-2-naphthoyl-CoA synthase
Similarity search - Component
Biological speciesMycobacterium tuberculosis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.15 Å
AuthorsJohnston, J.M. / Arcus, V.L. / Baker, E.N. / TB Structural Genomics Consortium (TBSGC)
CitationJournal: Acta Crystallogr.,Sect.D / Year: 2005
Title: Structure of naphthoate synthase (MenB) from Mycobacterium tuberculosis in both native and product-bound forms.
Authors: Johnston, J.M. / Arcus, V.L. / Baker, E.N.
History
DepositionNov 19, 2003Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 30, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Jul 21, 2021Group: Advisory / Database references / Derived calculations
Category: citation / pdbx_unobs_or_zero_occ_atoms ...citation / pdbx_unobs_or_zero_occ_atoms / struct_ref_seq_dif / struct_site
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Aug 23, 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

Downloads & links

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Assembly

Deposited unit
A: MenB
B: MenB
C: MenB
hetero molecules


Theoretical massNumber of molelcules
Total (without water)113,7494
Polymers113,4973
Non-polymers2521
Water3,819212
1
A: MenB
B: MenB
C: MenB
hetero molecules

A: MenB
B: MenB
C: MenB
hetero molecules


Theoretical massNumber of molelcules
Total (without water)227,4988
Polymers226,9946
Non-polymers5052
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_556y,x,-z+11
Buried area24650 Å2
ΔGint-106 kcal/mol
Surface area42730 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)80.305, 80.305, 257.553
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212
DetailsThe biological assembly is a hexamer generated from the trimer in the asymmetric unit by the operations: y, x, -z

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Components

#1: Protein MenB / Naphthoate synthase


Mass: 37832.270 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium tuberculosis (bacteria) / Gene: MenB / Plasmid: pProEX Hta / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 pRI592
References: UniProt: O06414, UniProt: P9WNP5*PLUS, 1,4-dihydroxy-2-naphthoyl-CoA synthase
#2: Chemical ChemComp-EP1 / 3-[4-(2-HYDROXYETHYL)PIPERAZIN-1-YL]PROPANE-1-SULFONIC ACID / HEPPS (buffer)


Mass: 252.331 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C9H20N2O4S / Comment: pH buffer*YM
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 212 / 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: 1.83 Å3/Da / Density % sol: 32.76 %
Crystal growTemperature: 291.15 K / Method: vapor diffusion, hanging drop / pH: 7.9
Details: MPEG 5K, EPPS , pH 7.9, VAPOR DIFFUSION, HANGING DROP, temperature 291.15K

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Data collection

DiffractionMean temperature: 113 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X8C / Wavelength: 1.1 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Feb 8, 2002
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.1 Å / Relative weight: 1
ReflectionResolution: 2.15→30 Å / Num. all: 47221 / Num. obs: 47207 / % possible obs: 99.97 % / Redundancy: 9.6 % / Biso Wilson estimate: 17.5 Å2 / Rmerge(I) obs: 0.114 / Net I/σ(I): 22.6
Reflection shellResolution: 2.15→2.23 Å / Rmerge(I) obs: 0.772 / Mean I/σ(I) obs: 3 / Num. unique all: 4638 / % possible all: 99.93

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Processing

Software
NameVersionClassification
CNS1.1refinement
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1DUB

1dub


Resolution: 2.15→29.88 Å / Rfactor Rfree error: 0.003 / Data cutoff high absF: 176238.15 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.231 4562 10.1 %RANDOM
Rwork0.203 ---
all-46995 --
obs-45158 96.1 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 47.6626 Å2 / ksol: 0.35744 e/Å3
Displacement parametersBiso mean: 28.6 Å2
Baniso -1Baniso -2Baniso -3
1-0.27 Å20 Å20 Å2
2--0.27 Å20 Å2
3----0.53 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.29 Å0.24 Å
Luzzati d res low-5 Å
Luzzati sigma a0.28 Å0.22 Å
Refinement stepCycle: LAST / Resolution: 2.15→29.88 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5599 0 16 212 5827
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.007
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.3
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d22.3
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.83
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it1.331.5
X-RAY DIFFRACTIONc_mcangle_it2.172
X-RAY DIFFRACTIONc_scbond_it1.972
X-RAY DIFFRACTIONc_scangle_it2.912.5
LS refinement shellResolution: 2.15→2.28 Å / Rfactor Rfree error: 0.011 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.302 695 10 %
Rwork0.254 6262 -
obs--90.5 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2WATER_REP.PARAMWATER.TOP
X-RAY DIFFRACTION3EPPSXPLODCNS.PARAMEPPSXPLODCNS.TOP

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