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- PDB-3oi9: Crystal structure of molybdenum cofactor synthesis domain from My... -

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Basic information

Entry
Database: PDB / ID: 3oi9
TitleCrystal structure of molybdenum cofactor synthesis domain from Mycobacterium avium
ComponentsMolybdenum cofactor synthesis domain
KeywordsBIOSYNTHETIC PROTEIN / Seattle Structural Genomics Center for Infectious Disease / SSGCID / mycobacterium / tuberculosis / paratubercluosis / molybdenum cofactor / moco
Function / homology
Function and homology information


Mo-molybdopterin cofactor biosynthetic process
Similarity search - Function
: / 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 / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Molybdenum cofactor synthesis domain / Molybdenum cofactor synthesis domain
Similarity search - Component
Biological speciesMycobacterium avium (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.95 Å
AuthorsSeattle Structural Genomics Center for Infectious Disease (SSGCID)
CitationJournal: Tuberculosis (Edinb) / Year: 2015
Title: Increasing the structural coverage of tuberculosis drug targets.
Authors: Baugh, L. / Phan, I. / Begley, D.W. / Clifton, M.C. / Armour, B. / Dranow, D.M. / Taylor, B.M. / Muruthi, M.M. / Abendroth, J. / Fairman, J.W. / Fox, D. / Dieterich, S.H. / Staker, B.L. / ...Authors: Baugh, L. / Phan, I. / Begley, D.W. / Clifton, M.C. / Armour, B. / Dranow, D.M. / Taylor, B.M. / Muruthi, M.M. / Abendroth, J. / Fairman, J.W. / Fox, D. / Dieterich, S.H. / Staker, B.L. / Gardberg, A.S. / Choi, R. / Hewitt, S.N. / Napuli, A.J. / Myers, J. / Barrett, L.K. / Zhang, Y. / Ferrell, M. / Mundt, E. / Thompkins, K. / Tran, N. / Lyons-Abbott, S. / Abramov, A. / Sekar, A. / Serbzhinskiy, D. / Lorimer, D. / Buchko, G.W. / Stacy, R. / Stewart, L.J. / Edwards, T.E. / Van Voorhis, W.C. / Myler, P.J.
History
DepositionAug 18, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 1, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Apr 22, 2015Group: Database references
Revision 1.3Sep 6, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Molybdenum cofactor synthesis domain


Theoretical massNumber of molelcules
Total (without water)16,6661
Polymers16,6661
Non-polymers00
Water1,42379
1
A: Molybdenum cofactor synthesis domain

A: Molybdenum cofactor synthesis domain

A: Molybdenum cofactor synthesis domain


Theoretical massNumber of molelcules
Total (without water)49,9973
Polymers49,9973
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_565-y,x-y+1,z1
crystal symmetry operation3_455-x+y-1,-x,z1
Buried area3510 Å2
ΔGint-29 kcal/mol
Surface area18100 Å2
MethodPISA
Unit cell
Length a, b, c (Å)68.030, 68.030, 53.170
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number173
Space group name H-MP63

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Components

#1: Protein Molybdenum cofactor synthesis domain


Mass: 16665.645 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium avium (bacteria) / Strain: 104 / Gene: MAV_0994 / Plasmid: AVA0421 / Production host: Escherichia coli (E. coli) / References: UniProt: A0QBG6, UniProt: A0A0H2ZWD1*PLUS
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 79 / 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: 2.13 Å3/Da / Density % sol: 42.29 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 5
Details: 29.9 mg/mL MyavA.00778.b.A1 PW28925 against EBS PACT screen condition A8, 0.2 M ammonium chloride, 0.1 M sodium acetate pH 5.0, 20% PEG 6000 with 25% ethylene glycol as cryo-protectant, ...Details: 29.9 mg/mL MyavA.00778.b.A1 PW28925 against EBS PACT screen condition A8, 0.2 M ammonium chloride, 0.1 M sodium acetate pH 5.0, 20% PEG 6000 with 25% ethylene glycol as cryo-protectant, crystal tracking ID 217062a8, VAPOR DIFFUSION, SITTING DROP

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU FR-E+ SUPERBRIGHT / Wavelength: 1.5418 Å
DetectorType: RIGAKU SATURN 944+ / Detector: CCD / Date: Aug 12, 2010
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.95→50 Å / Num. all: 10314 / Num. obs: 10275 / % possible obs: 99.6 % / Observed criterion σ(I): -3 / Redundancy: 3.9 % / Biso Wilson estimate: 33.744 Å2 / Rmerge(I) obs: 0.046 / Net I/σ(I): 19.07
Reflection shell

Diffraction-ID: 1

Resolution (Å)Highest resolution (Å)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. unique obs% possible all
1.95-20.4412174276599.6
2-2.060.362.8187673599.5
2.06-2.120.2574.1201870699
2.12-2.180.186217168899.9
2.18-2.250.1677.4228067299.4
2.25-2.330.1737.7234765299.4
2.33-2.420.1419.5248162899.8
2.42-2.520.10912.9279762199.7
2.52-2.630.09814263456599.8
2.63-2.760.0816.62637568100
2.76-2.910.06120.2245152199.8
2.91-3.080.05821.5243852099.8
3.08-3.30.04327.52196466100
3.3-3.560.03140.82093445100
3.56-3.90.0346.2186240299.8
3.9-4.360.02452.4175037499.7
4.36-5.040.02158.5149532499.7
5.04-6.170.02447.21338286100
6.17-8.720.01855.8993217100
8.720.0177050012094.5

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Phasing

PhasingMethod: molecular replacement
Phasing MRRfactor: 42.57 / Model details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation3.2 Å29.46 Å
Translation3.2 Å29.46 Å

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Processing

Software
NameVersionClassificationNB
XSCALEdata scaling
PHASER2.1.4phasing
REFMACrefinement
PDB_EXTRACT3.1data extraction
StructureStudiodata collection
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2g4r molecule a

2g4r


Resolution: 1.95→50 Å / Cor.coef. Fo:Fc: 0.95 / Cor.coef. Fo:Fc free: 0.925 / WRfactor Rfree: 0.224 / WRfactor Rwork: 0.1741 / Occupancy max: 1 / Occupancy min: 0.5 / FOM work R set: 0.8485 / SU B: 12.047 / SU ML: 0.138 / SU R Cruickshank DPI: 0.0381 / SU Rfree: 0.0349 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.035 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES: WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.2446 493 4.8 %RANDOM
Rwork0.1962 ---
obs0.1987 10254 99.43 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso max: 85.89 Å2 / Biso mean: 40.3835 Å2 / Biso min: 16.51 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refinement stepCycle: LAST / Resolution: 1.95→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1032 0 0 79 1111
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0221057
X-RAY DIFFRACTIONr_angle_refined_deg1.3611.991453
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.625153
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.19325.15233
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.53115145
X-RAY DIFFRACTIONr_dihedral_angle_4_deg11.838156
X-RAY DIFFRACTIONr_chiral_restr0.0880.2184
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.022797
X-RAY DIFFRACTIONr_mcbond_it0.7131.5749
X-RAY DIFFRACTIONr_mcangle_it1.26221197
X-RAY DIFFRACTIONr_scbond_it1.9853308
X-RAY DIFFRACTIONr_scangle_it3.4454.5254
LS refinement shellResolution: 1.95→2 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.396 35 -
Rwork0.285 714 -
all-749 -
obs--99.21 %
Refinement TLS params.Method: refined / Origin x: -18.8311 Å / Origin y: 11.3596 Å / Origin z: -9.0971 Å
111213212223313233
T0.1072 Å20.0081 Å20.0111 Å2-0.0807 Å20.0126 Å2--0.0045 Å2
L3.3109 °2-0.4364 °2-0.0154 °2-1.6179 °2-0.7595 °2--1.3618 °2
S0.1511 Å °-0.114 Å °0.0641 Å °-0.0983 Å °-0.1754 Å °-0.0398 Å °0.1398 Å °0.0774 Å °0.0243 Å °

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