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- PDB-2nqq: MoeA R137Q -

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Basic information

Entry
Database: PDB / ID: 2nqq
TitleMoeA R137Q
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: 2.4 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 / Category: chem_comp_atom / chem_comp_bond

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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
C: Molybdopterin biosynthesis protein moeA
D: Molybdopterin biosynthesis protein moeA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)177,59718
Polymers176,3084
Non-polymers1,28914
Water15,151841
1
A: Molybdopterin biosynthesis protein moeA
B: Molybdopterin biosynthesis protein moeA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)88,89110
Polymers88,1542
Non-polymers7378
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6910 Å2
ΔGint-39 kcal/mol
Surface area33700 Å2
MethodPISA
2
C: Molybdopterin biosynthesis protein moeA
D: Molybdopterin biosynthesis protein moeA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)88,7078
Polymers88,1542
Non-polymers5536
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6580 Å2
ΔGint-41 kcal/mol
Surface area34140 Å2
MethodPISA
Unit cell
Length a, b, c (Å)80.205, 106.644, 99.691
Angle α, β, γ (deg.)90.00, 91.57, 90.00
Int Tables number4
Space group name H-MP1211
DetailsDimers of chains A/B and C/D

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Components

#1: Protein
Molybdopterin biosynthesis protein moeA


Mass: 44076.996 Da / Num. of mol.: 4 / Mutation: R137Q
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.: 14 / Source method: obtained synthetically / Formula: C3H8O3
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 841 / 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: 2.42 Å3/Da / Density % sol: 49.09 %
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 22, 2001
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.1 Å / Relative weight: 1
ReflectionResolution: 2.4→50 Å / Num. all: 62414 / Num. obs: 60480 / % possible obs: 96.9 % / 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: 2.4→50 Å / Cor.coef. Fo:Fc: 0.945 / Cor.coef. Fo:Fc free: 0.902 / SU B: 8.799 / SU ML: 0.207 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.593 / ESU R Free: 0.299 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.261 3157 5 %RANDOM
Rwork0.19 ---
all0.193 62414 --
obs0.193 60480 96.92 %-
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: 36.556 Å2
Baniso -1Baniso -2Baniso -3
1--1.2 Å20 Å2-0.87 Å2
2--1.45 Å20 Å2
3----0.3 Å2
Refinement stepCycle: LAST / Resolution: 2.4→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms12152 0 84 841 13077
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0170.02112462
X-RAY DIFFRACTIONr_bond_other_d0.0020.0211558
X-RAY DIFFRACTIONr_angle_refined_deg1.681.96916914
X-RAY DIFFRACTIONr_angle_other_deg0.913326842
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.77951608
X-RAY DIFFRACTIONr_chiral_restr0.0960.21928
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0214020
X-RAY DIFFRACTIONr_gen_planes_other0.0020.022440
X-RAY DIFFRACTIONr_nbd_refined0.2230.22745
X-RAY DIFFRACTIONr_nbd_other0.2490.213942
X-RAY DIFFRACTIONr_nbtor_other0.0920.28092
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2170.2681
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2120.245
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2980.2155
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1740.224
X-RAY DIFFRACTIONr_mcbond_it0.9721.57992
X-RAY DIFFRACTIONr_mcangle_it1.842212848
X-RAY DIFFRACTIONr_scbond_it2.5634470
X-RAY DIFFRACTIONr_scangle_it4.5244.54066
LS refinement shellResolution: 2.4→2.462 Å / Total num. of bins used: 20
RfactorNum. reflection
Rfree0.291 244
Rwork0.225 4500
obs-4744
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)
10.62010.237-0.96680.4062-0.09971.09620.1596-0.04580.06580.0138-0.0854-0.0099-0.08880.005-0.07420.00890.0001-0.00010.008900.00932.1979-13.549239.9371
20.1063-0.03320.12952.05861.70043.3135-0.02370.1419-0.20630.0098-0.07-0.0698-0.2591-0.25590.09380.0089000.008900.008933.20629.2902-41.8327
34.63350.78862.0812-0.69162.04772.3172-0.0053-0.41660.1159-0.0235-0.1460.04420.0603-0.24480.15120.009000.00880.00010.0089-0.08341.443396.8516
42.8385-0.87750.56310.0615-1.39843.4792-0.0010.5083-0.00360.0034-0.003-0.04190.08290.06090.0040.0089000.008800.0096.995715.49388.9876
50.0358-0.0147-0.0440.01520.02510.0427-0.004-0.0136-0.0059-0.0106-0.0050.0102-0.00430.00830.0090.0097-0.00560.00130.01050.00520.00620.277410.372926.2772
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
33CC53 - 14053 - 140
44DD53 - 14053 - 140
55AA7 - 527 - 52
65BB7 - 527 - 52
75CC7 - 527 - 52
85DD7 - 527 - 52
95AA141 - 409141 - 409
105BB141 - 409141 - 409
115CC141 - 409141 - 409
125DD141 - 409141 - 409

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