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- PDB-2nqk: MoeA D59N mutant -

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Basic information

Entry
Database: PDB / ID: 2nqk
TitleMoeA D59N mutant
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 / metal ion binding / identical protein binding / cytoplasm / cytosol
Similarity search - Function
Molybdopterin biosynthesis moeA protein; domain 3 / Molybdopterin biosynthesis moea protein, domain 3. / Beta-clip / MoeA, C-terminal, domain IV / Molybdopterin biosynthesis moea protein, domain 2 / Molybdenum cofactor biosynthesis proteins signature 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 / Molybdopterin biosynthesis moea protein, domain 2 / Molybdenum cofactor biosynthesis proteins signature 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: 2.9 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
DepositionOct 31, 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)88,2102
Polymers88,2102
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4390 Å2
ΔGint-29 kcal/mol
Surface area35080 Å2
MethodPISA
Unit cell
Length a, b, c (Å)89.192, 98.219, 99.745
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
DetailsDimer of chain A and B

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Components

#1: Protein Molybdopterin biosynthesis protein moeA


Mass: 44105.074 Da / Num. of mol.: 2 / Mutation: D59N
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: 2.48 Å3/Da / Density % sol: 50.3 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 10-15% PEG 6000 or PEG 8000, 0.2-0.5 M calcium acetate, 0.1 M cacodylic acid, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 298.0K

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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: Oct 16, 2001
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.1 Å / Relative weight: 1
ReflectionResolution: 2.9→50 Å / Num. all: 19252 / Num. obs: 18278 / % possible obs: 96.2 % / 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: 2.9→50 Å / Cor.coef. Fo:Fc: 0.916 / Cor.coef. Fo:Fc free: 0.847 / SU B: 17.603 / SU ML: 0.324 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.459 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.266 974 5.1 %RANDOM
Rwork0.198 ---
all0.201 19252 --
obs0.201 18278 96.21 %-
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: 22.535 Å2
Baniso -1Baniso -2Baniso -3
1-0.83 Å20 Å20 Å2
2---1.27 Å20 Å2
3---0.44 Å2
Refinement stepCycle: LAST / Resolution: 2.9→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6080 0 0 0 6080
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.0216200
X-RAY DIFFRACTIONr_bond_other_d0.0020.025758
X-RAY DIFFRACTIONr_angle_refined_deg1.511.9648426
X-RAY DIFFRACTIONr_angle_other_deg0.869313356
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.2325804
X-RAY DIFFRACTIONr_chiral_restr0.0830.2964
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.027012
X-RAY DIFFRACTIONr_gen_planes_other0.0020.021228
X-RAY DIFFRACTIONr_nbd_refined0.2140.21221
X-RAY DIFFRACTIONr_nbd_other0.240.26601
X-RAY DIFFRACTIONr_nbtor_other0.0910.24061
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.120.289
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2650.226
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2720.289
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1180.22
X-RAY DIFFRACTIONr_mcbond_it1.0711.53996
X-RAY DIFFRACTIONr_mcangle_it2.0926424
X-RAY DIFFRACTIONr_scbond_it2.6532204
X-RAY DIFFRACTIONr_scangle_it4.8114.52002
LS refinement shellResolution: 2.9→2.975 Å / Total num. of bins used: 20
RfactorNum. reflection
Rfree0.313 64
Rwork0.274 1229
obs-1293
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)
11.54541.1308-0.17792.52540.30830.72140.08880.0011-0.08060.0617-0.0422-0.06390.02590.007-0.04660.09390.0006-0.01310.0939-0.03040.0978-26.16551.9579-4.3179
21.61541.1201-0.50726.7343-2.61394.0835-0.08640.1457-0.09210.10990.09760.2605-0.2178-0.0402-0.01110.021-0.01210.00360.0217-0.01010.0214-29.125789.283621.8021
30.34660.2564-0.10860.432-0.00360.1013-0.01430.03470.02560.06010.0380.0703-0.0247-0.0053-0.02370.08520.0104-0.00330.09970.01890.0848-19.784844.050414.3126
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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