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- PDB-2nrs: MoeA S371W -

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Basic information

Entry
Database: PDB / ID: 2nrs
TitleMoeA S371W
ComponentsMolybdopterin biosynthesis protein moeA
KeywordsBIOSYNTHETIC PROTEIN / molybdopterin / MPT / Moco / molybdenum / MoeA / MogA / gephyrin / Cnx1 / cinnamon
Function / homology
Function and homology information


molybdopterin molybdotransferase / molybdopterin molybdotransferase activity / Mo-molybdopterin cofactor biosynthetic process / protein homodimerization activity / identical protein binding / metal ion binding / cytosol / cytoplasm
Similarity search - Function
Molybdopterin biosynthesis moeA protein; domain 3 / Molybdopterin biosynthesis moea protein, domain 3. / Beta-clip / MoeA, C-terminal, domain IV / Molybdenum cofactor biosynthesis proteins signature 2. / Molybdopterin biosynthesis moea protein, domain 2 / MoeA, N-terminal and linker domain / MoeA, C-terminal, domain IV / MoeA, N-terminal and linker domain superfamily / MoeA, C-terminal, domain IV superfamily ...Molybdopterin biosynthesis moeA protein; domain 3 / Molybdopterin biosynthesis moea protein, domain 3. / Beta-clip / MoeA, C-terminal, domain IV / Molybdenum cofactor biosynthesis proteins signature 2. / Molybdopterin biosynthesis moea protein, domain 2 / MoeA, N-terminal and linker domain / MoeA, C-terminal, domain IV / MoeA, N-terminal and linker domain superfamily / MoeA, C-terminal, domain IV superfamily / Molybdopterin biosynthesis protein MoeA-like / MoeA N-terminal region (domain I and II) / MoeA C-terminal region (domain IV) / Molybdopterin biosynthesis moea protein, domain 2 / Molybdenum cofactor biosynthesis, conserved site / MoaB/Mog-like domain / Molybdenum Cofactor Biosythetic Enzyme; Chain A / MoaB/Mog domain / MoaB/Mog-like domain superfamily / Probable molybdopterin binding domain / Probable molybdopterin binding domain / Beta Complex / Alpha-Beta Complex / Beta Barrel / 3-Layer(aba) Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
Molybdopterin molybdenumtransferase
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.8 Å
AuthorsNicolas, J. / Xiang, S. / Schindelin, H. / Rajagopalan, K.V.
CitationJournal: Biochemistry / Year: 2007
Title: Mutational Analysis of Escherichia coli MoeA: Two Functional Activities Map to the Active Site Cleft.
Authors: Nichols, J.D. / Xiang, S. / Schindelin, H. / Rajagopalan, K.V.
History
DepositionNov 2, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 16, 2007Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 20, 2021Group: Database references / Category: database_2 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details
Revision 1.4Dec 27, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Molybdopterin biosynthesis protein moeA
B: Molybdopterin biosynthesis protein moeA


Theoretical massNumber of molelcules
Total (without water)88,4102
Polymers88,4102
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4770 Å2
ΔGint-30 kcal/mol
Surface area34200 Å2
MethodPISA
Unit cell
Length a, b, c (Å)68.485, 98.714, 159.735
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
DetailsDimer of Chains A and B

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Components

#1: Protein Molybdopterin biosynthesis protein moeA


Mass: 44205.191 Da / Num. of mol.: 2 / Mutation: S371W
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: moeA, bisB, chlE, narE / Plasmid: pET11a / Production host: Escherichia coli (E. coli) / Strain (production host): AH69 (DE3) / References: UniProt: P12281

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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: 3.05 Å3/Da / Density % sol: 59.7 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 10%-15% PEG 6000/8000, 0.2-0.5 M calcium acetate, 0.1 M cacodylic acid, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X26C / Wavelength: 1.1
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Jul 23, 2002
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.1 Å / Relative weight: 1
ReflectionResolution: 2.8→50 Å / Num. all: 25990 / Num. obs: 25644 / Observed criterion σ(F): 2 / Observed criterion σ(I): 2

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Processing

Software
NameVersionClassificationNB
REFMAC5.1.24refinement
PDB_EXTRACT2data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.8→49.39 Å / Cor.coef. Fo:Fc: 0.91 / Cor.coef. Fo:Fc free: 0.858 / SU B: 16.687 / SU ML: 0.316 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 1.563 / ESU R Free: 0.423 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.303 1377 5.1 %RANDOM
Rwork0.247 ---
all0.25 25990 --
obs0.25 25644 98.67 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 32.263 Å2
Baniso -1Baniso -2Baniso -3
1-6.87 Å20 Å20 Å2
2---5.12 Å20 Å2
3----1.74 Å2
Refinement stepCycle: LAST / Resolution: 2.8→49.39 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6096 0 0 0 6096
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0180.0216220
X-RAY DIFFRACTIONr_bond_other_d0.0020.025770
X-RAY DIFFRACTIONr_angle_refined_deg1.7371.9638456
X-RAY DIFFRACTIONr_angle_other_deg0.893313380
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.0845804
X-RAY DIFFRACTIONr_chiral_restr0.0870.2964
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.027032
X-RAY DIFFRACTIONr_gen_planes_other0.0020.021238
X-RAY DIFFRACTIONr_nbd_refined0.2430.21407
X-RAY DIFFRACTIONr_nbd_other0.2460.26941
X-RAY DIFFRACTIONr_nbtor_other0.0970.24225
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1590.294
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.3390.218
X-RAY DIFFRACTIONr_symmetry_vdw_other0.1860.242
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.3350.22
X-RAY DIFFRACTIONr_mcbond_it0.8461.53996
X-RAY DIFFRACTIONr_mcangle_it1.67626424
X-RAY DIFFRACTIONr_scbond_it2.40432224
X-RAY DIFFRACTIONr_scangle_it4.4124.52032
LS refinement shellResolution: 2.8→2.873 Å / Total num. of bins used: 20
RfactorNum. reflection
Rfree0.454 107
Rwork0.332 1662
obs-1769
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)
14.00274.07561.12238.44315.75575.490.1401-0.24220.22260.0181-0.32580.3085-0.2394-0.06560.18580.1394000.139500.139430.793979.829365.84
22.5338-0.326-0.87544.0468-0.54740.3539-0.05580.028-0.1601-0.27910.0239-0.30360.07020.09690.03180.13650.02770.10560.1098-0.060.14533.7428-6.751166.1274
30.29820.14330.16270.69630.17520.3540.0135-0.0137-0.07550.02050.085-0.0954-0.05870.0022-0.09850.04650.00060.00040.12940.00680.090710.554337.935859.7411
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION / Selection: ALL

IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11AA53 - 14053 - 140
22BB53 - 14053 - 140
33AA7 - 527 - 52
43BB7 - 527 - 52
53AA141 - 409141 - 409
63BB141 - 409141 - 409

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