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- PDB-2nqn: MoeA T100W -

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Basic information

Entry
Database: PDB / ID: 2nqn
TitleMoeA T100W
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: 2.2 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: Non-polymer description / Version format compliance
Revision 1.3Oct 20, 2021Group: Database references / Derived calculations / Category: database_2 / 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
Revision 1.4Dec 27, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / struct_ncs_dom_lim
Item: _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.end_auth_comp_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)91,05331
Polymers88,3822
Non-polymers2,67129
Water8,539474
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area11150 Å2
ΔGint-36 kcal/mol
Surface area34100 Å2
MethodPISA
Unit cell
Length a, b, c (Å)69.079, 98.659, 158.997
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
31A
41B
51A
61B

NCS domain segments:

Ens-ID: 1

Dom-IDComponent-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDRefine codeAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11LEULEUVALVAL3AA7 - 507 - 50
21LEULEUVALVAL3BB7 - 507 - 50
32GLUGLUGLYGLY3AA141 - 409141 - 409
42GLUGLUGLYGLY3BB141 - 409141 - 409
53PROPROGLYGLY6AA51 - 14051 - 140
63PROPROGLYGLY6BB51 - 14051 - 140
DetailsDimer of chain A and B

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Components

#1: Protein Molybdopterin biosynthesis protein moeA


Mass: 44191.164 Da / Num. of mol.: 2 / Mutation: T100W
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
#2: Chemical...
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 29 / Source method: obtained synthetically / Formula: C3H8O3
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 474 / 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: 3.06 Å3/Da / Density % sol: 59.85 %
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: Apr 16, 2001
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.1 Å / Relative weight: 1
ReflectionResolution: 2.2→50 Å / Num. all: 51582 / Num. obs: 51582 / % possible obs: 100 % / 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: 2.2→49.39 Å / Cor.coef. Fo:Fc: 0.943 / Cor.coef. Fo:Fc free: 0.915 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.264 / ESU R Free: 0.222 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.274 2786 5.1 %RANDOM
Rwork0.225 ---
all0.228 51582 --
obs0.228 51582 100 %-
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: 42.951 Å2
Baniso -1Baniso -2Baniso -3
1-5.98 Å20 Å20 Å2
2---3.87 Å20 Å2
3----2.11 Å2
Refinement stepCycle: LAST / Resolution: 2.2→49.39 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6110 0 174 474 6758
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0216379
X-RAY DIFFRACTIONr_bond_other_d00.025923
X-RAY DIFFRACTIONr_angle_refined_deg1.4931.9818617
X-RAY DIFFRACTIONr_angle_other_deg3.529313777
X-RAY DIFFRACTIONr_dihedral_angle_1_deg1.2595808
X-RAY DIFFRACTIONr_chiral_restr0.1040.2962
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.027060
X-RAY DIFFRACTIONr_gen_planes_other0.0050.021242
X-RAY DIFFRACTIONr_nbd_refined0.2320.21455
X-RAY DIFFRACTIONr_nbd_other0.3170.26918
X-RAY DIFFRACTIONr_nbtor_other0.1130.23478
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.160.2387
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.3370.240
X-RAY DIFFRACTIONr_symmetry_vdw_other0.350.299
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2440.218
X-RAY DIFFRACTIONr_mcbond_it3.081.54012
X-RAY DIFFRACTIONr_mcangle_it4.83426442
X-RAY DIFFRACTIONr_scbond_it5.34132367
X-RAY DIFFRACTIONr_scangle_it7.3874.52175
Refine LS restraints NCS

Dom-ID: 1 / Auth asym-ID: A / Ens-ID: 1 / Refine-ID: X-RAY DIFFRACTION

NumberTypeRms dev position (Å)Weight position
1832TIGHT POSITIONAL0.060.05
4099LOOSE POSITIONAL2.495
1832TIGHT THERMAL1.840.5
4099LOOSE THERMAL6.9810
LS refinement shellResolution: 2.2→2.257 Å / Total num. of bins used: 20
RfactorNum. reflection
Rfree0.377 199
Rwork0.358 3416
obs-3615

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