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- PDB-2nqr: MoeA D142N -

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Basic information

Entry
Database: PDB / ID: 2nqr
TitleMoeA D142N
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 / cytosol / cytoplasm
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: 2.2 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_conn ...database_2 / 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 / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_asym_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_asym_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_conn.ptnr2_label_seq_id / _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 / Category: chem_comp_atom / chem_comp_bond
Revision 1.5Dec 25, 2024Group: Advisory / Derived calculations / Structure summary
Category: pdbx_distant_solvent_atoms / pdbx_entry_details ...pdbx_distant_solvent_atoms / pdbx_entry_details / pdbx_validate_close_contact / struct_conn

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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)89,86820
Polymers88,2102
Non-polymers1,65818
Water15,115839
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9750 Å2
ΔGint-41 kcal/mol
Surface area33450 Å2
MethodPISA
Unit cell
Length a, b, c (Å)75.284, 100.076, 102.485
Angle α, β, γ (deg.)90.00, 90.00, 90.00
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: 44105.074 Da / Num. of mol.: 2 / Mutation: D142N
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


Mass: 92.094 Da / Num. of mol.: 18 / Source method: obtained synthetically / Formula: C3H8O3
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 839 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationN

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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: 2.19 Å3/Da / Density % sol: 43.76 %
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: Oct 18, 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: 37995 / Num. obs: 37554 / % possible obs: 98.8 % / 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→45.64 Å / Cor.coef. Fo:Fc: 0.956 / Cor.coef. Fo:Fc free: 0.893 / SU B: 6.279 / SU ML: 0.159 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.314 / ESU R Free: 0.246 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.253 1981 5 %RANDOM
Rwork0.162 ---
all0.166 37995 --
obs0.166 37554 98.84 %-
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: 18.057 Å2
Baniso -1Baniso -2Baniso -3
1--0.5 Å20 Å20 Å2
2---0.67 Å20 Å2
3---1.16 Å2
Refinement stepCycle: LAST / Resolution: 2.2→45.64 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6084 0 108 839 7031
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.020.0216294
X-RAY DIFFRACTIONr_bond_other_d0.0030.025851
X-RAY DIFFRACTIONr_angle_refined_deg1.9631.9758521
X-RAY DIFFRACTIONr_angle_other_deg0.969313597
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.6855805
X-RAY DIFFRACTIONr_chiral_restr0.1180.2964
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.027019
X-RAY DIFFRACTIONr_gen_planes_other0.0020.021229
X-RAY DIFFRACTIONr_nbd_refined0.2320.21371
X-RAY DIFFRACTIONr_nbd_other0.2650.27145
X-RAY DIFFRACTIONr_nbtor_other0.0930.24066
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2260.2585
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2930.246
X-RAY DIFFRACTIONr_symmetry_vdw_other0.3330.2135
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2910.244
X-RAY DIFFRACTIONr_mcbond_it0.981.54000
X-RAY DIFFRACTIONr_mcangle_it1.82426429
X-RAY DIFFRACTIONr_scbond_it3.04732294
X-RAY DIFFRACTIONr_scangle_it5.1354.52092
LS refinement shellResolution: 2.2→2.257 Å / Total num. of bins used: 20
RfactorNum. reflection
Rfree0.274 120
Rwork0.205 2757
obs-2877
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)
11.14040.5344-0.38220.7376-0.1040.380.0921-0.11470.04570.0139-0.05240.0411-0.0010.0449-0.03980.0276-0.01370.00710.02710.00070.002823.110291.96963.2129
20.45270.07990.06221.50850.17860.4968-0.03850.0658-0.01650.02870.0733-0.0640.0387-0.0121-0.03470.0167-0.0053-0.00690.0112-0.00170.019822.65224.631328.3296
30.0850.03020.00910.2219-0.01580.0213-0.01290.02030.0035-0.00220.0137-0.01510.00920.0084-0.00080.0195-0.001-0.00160.0265-0.00160.011919.344848.570817.2192
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 - 410141 - 410
63BB141 - 409141 - 409

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