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- PDB-3rfq: Crystal structure of Pterin-4-alpha-carbinolamine dehydratase Moa... -

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Basic information

Entry
Database: PDB / ID: 3rfq
TitleCrystal structure of Pterin-4-alpha-carbinolamine dehydratase MoaB2 from Mycobacterium marinum
ComponentsPterin-4-alpha-carbinolamine dehydratase MoaB2
KeywordsBIOSYNTHETIC PROTEIN / Structural Genomics / Seattle Structural Genomics Center for Infectious Disease / SSGCID / ortholog / Mycobacterium / tuberculosis / water contaminant / cofactor iosynthesis / molybdenum cofactor / GTP / pterin
Function / homologyMoaB/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 / Pterin-4-alpha-carbinolamine dehydratase MoaB2
Function and homology information
Biological speciesMycobacterium marinum (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.25 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
DepositionApr 6, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 4, 2011Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Apr 22, 2015Group: Database references
Revision 1.3Sep 13, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / pdbx_struct_special_symmetry / struct_conn / struct_ncs_dom_lim / 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 / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _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_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Pterin-4-alpha-carbinolamine dehydratase MoaB2
B: Pterin-4-alpha-carbinolamine dehydratase MoaB2
C: Pterin-4-alpha-carbinolamine dehydratase MoaB2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)56,4436
Polymers56,1153
Non-polymers3283
Water5,170287
1
A: Pterin-4-alpha-carbinolamine dehydratase MoaB2
B: Pterin-4-alpha-carbinolamine dehydratase MoaB2
C: Pterin-4-alpha-carbinolamine dehydratase MoaB2
hetero molecules

A: Pterin-4-alpha-carbinolamine dehydratase MoaB2
B: Pterin-4-alpha-carbinolamine dehydratase MoaB2
C: Pterin-4-alpha-carbinolamine dehydratase MoaB2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)112,88612
Polymers112,2306
Non-polymers6576
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_555-x,y,-z+1/21
Buried area11730 Å2
ΔGint-109 kcal/mol
Surface area32930 Å2
MethodPISA
Unit cell
Length a, b, c (Å)125.640, 137.640, 73.960
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number20
Space group name H-MC2221
Components on special symmetry positions
IDModelComponents
11C-181-

NA

21C-275-

HOH

31C-284-

HOH

41C-287-

HOH

Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
31C

NCS domain segments:

Component-ID: 1 / Ens-ID: 1 / Beg auth comp-ID: VAL / Beg label comp-ID: VAL / End auth comp-ID: ILE / End label comp-ID: ILE / Refine code: 5 / Auth seq-ID: 25 - 173 / Label seq-ID: 30 - 178

Dom-IDAuth asym-IDLabel asym-ID
1AA
2BB
3CC

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Components

#1: Protein Pterin-4-alpha-carbinolamine dehydratase MoaB2


Mass: 18704.920 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium marinum (bacteria) / Strain: ATCC BAA-535/M / Gene: MMAR_4526, moaB2 / Plasmid: pAVA0421 / Production host: Escherichia coli (E. coli) / References: UniProt: B2HEA7
#2: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Na
#3: Chemical ChemComp-B3P / 2-[3-(2-HYDROXY-1,1-DIHYDROXYMETHYL-ETHYLAMINO)-PROPYLAMINO]-2-HYDROXYMETHYL-PROPANE-1,3-DIOL / Bis-tris propane


Mass: 282.334 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C11H26N2O6 / Comment: pH buffer*YM
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 287 / 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: 2.85 Å3/Da / Density % sol: 56.83 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: MymaA.00778.a.A1 PS00869 at 45.9 mg/mL against PACT screen condition G10 20 mM Na/K phosphate, 0.1 M BisTris Propane pH 7.5, 20% PEG 3350 with 25% ethylene glycol as cryo-protection reagent, ...Details: MymaA.00778.a.A1 PS00869 at 45.9 mg/mL against PACT screen condition G10 20 mM Na/K phosphate, 0.1 M BisTris Propane pH 7.5, 20% PEG 3350 with 25% ethylene glycol as cryo-protection reagent, crsytal tracking ID 219070g10, VAPOR DIFFUSION, SITTING DROP, temperature 289K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.1 / Wavelength: 0.97946 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Mar 26, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97946 Å / Relative weight: 1
ReflectionResolution: 2.25→50 Å / Num. all: 30064 / Num. obs: 30064 / % possible obs: 97.5 % / Observed criterion σ(I): -3 / Redundancy: 6 % / Biso Wilson estimate: 30.055 Å2 / Rmerge(I) obs: 0.129 / Net I/σ(I): 10.14
Reflection shell

Diffraction-ID: 1

Resolution (Å)Highest resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. unique allNum. unique obs% possible all
2.25-2.315.20.413.8397451858185882.7
2.31-2.370.3614.2712091213597.5
2.37-2.440.3384.9813178210798.6
2.44-2.520.2785.9312856205998.4
2.52-2.60.2486.612252196498.4
2.6-2.690.2167.5911915191398.5
2.69-2.790.1878.5611552185498.6
2.79-2.90.1699.1711287181898.7
2.9-3.030.1659.6110529170298.7
3.03-3.180.13911.210181165798.9
3.18-3.350.11612.999638156998.5
3.35-3.560.10814.259017148398.8
3.56-3.80.099158446141599.1
3.8-4.110.09615.817781131598.9
4.11-4.50.08617.057207120599.3
4.5-5.030.08616.86707112199
5.03-5.810.09115.85578198899.3
5.81-7.120.0915.46483684299.3
7.12-10.060.07918.46384566799.1
10.060.08218.38207839296.8

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Phasing

PhasingMethod: molecular replacement
Phasing MRRfactor: 51.28 / Model details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation3 Å47.88 Å
Translation3 Å47.88 Å

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Processing

Software
NameVersionClassificationNB
XSCALEdata scaling
PHASER2.1.4phasing
REFMACrefinement
PDB_EXTRACT3.1data extraction
BOSdata collection
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3oi9

3oi9


Resolution: 2.25→50 Å / Cor.coef. Fo:Fc: 0.948 / Cor.coef. Fo:Fc free: 0.926 / WRfactor Rfree: 0.2022 / WRfactor Rwork: 0.1686 / Occupancy max: 1 / Occupancy min: 0.4 / FOM work R set: 0.8853 / SU B: 9.469 / SU ML: 0.107 / SU R Cruickshank DPI: 0.2026 / SU Rfree: 0.171 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.171 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : RESIDUAL ONLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2078 1502 5 %RANDOM
Rwork0.1727 ---
obs0.1745 29942 97.14 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso max: 97.36 Å2 / Biso mean: 25.7658 Å2 / Biso min: 2 Å2
Baniso -1Baniso -2Baniso -3
1--2.05 Å20 Å20 Å2
2--1.36 Å20 Å2
3---0.69 Å2
Refinement stepCycle: LAST / Resolution: 2.25→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3277 0 21 287 3585
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0223346
X-RAY DIFFRACTIONr_angle_refined_deg1.421.9844573
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.1045470
X-RAY DIFFRACTIONr_dihedral_angle_2_deg40.92124.132121
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.50915511
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.1511528
X-RAY DIFFRACTIONr_chiral_restr0.0930.2594
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0212463
X-RAY DIFFRACTIONr_mcbond_it0.6591.52285
X-RAY DIFFRACTIONr_mcangle_it1.1823664
X-RAY DIFFRACTIONr_scbond_it1.91331061
X-RAY DIFFRACTIONr_scangle_it3.1084.5905
Refine LS restraints NCS

Ens-ID: 1 / Refine-ID: X-RAY DIFFRACTION

Dom-IDAuth asym-IDNumberTypeRms dev position (Å)Weight position
1A596MEDIUM POSITIONAL0.140.5
2B596MEDIUM POSITIONAL0.130.5
3C596MEDIUM POSITIONAL0.110.5
1A454LOOSE POSITIONAL0.45
2B454LOOSE POSITIONAL0.395
3C454LOOSE POSITIONAL0.385
1A596MEDIUM THERMAL0.752
2B596MEDIUM THERMAL0.632
3C596MEDIUM THERMAL0.852
1A454LOOSE THERMAL1.1810
2B454LOOSE THERMAL0.9110
3C454LOOSE THERMAL1.0610
LS refinement shellResolution: 2.25→2.308 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.246 91 -
Rwork0.242 1757 -
all-1848 -
obs--82.39 %
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)
110.102-2.2844-1.05352.7308-0.8714.88540.16671.6585-0.2093-0.41540.08170.05530.3157-0.143-0.24840.1674-0.0341-0.00070.50060.0730.147110.5634-29.1138-8.5318
24.8321-0.1132-0.81941.1732-0.32871.2572-0.01040.35940.2915-0.1462-0.0258-0.116-0.03760.04290.03620.0489-0.02580.01220.12870.05870.045315.0952-30.0238-2.5106
32.31230.6498-0.19871.1954-0.11141.5164-0.00940.09460.206-0.01880.01140.0122-0.09230.0357-0.0020.02040.00220.01140.04080.02440.03979.9397-32.81477.6919
47.15010.9666-0.6892.00181.23214.82110.0889-0.50791.0116-0.2869-0.04860.3443-0.45510.2226-0.04030.0999-0.0454-0.00340.1684-0.13980.203519.669-25.337137.2399
53.1994-0.30920.62931.9177-0.15631.49310.0164-0.15150.20010.05410.0395-0.1272-0.13170.2344-0.05590.042-0.0362-0.02410.1042-0.03320.068122.6447-31.921331.9194
63.8092-0.6180.2711.73410.02341.1862-0.0158-0.08810.06950.09080.02680.00430.02130.0058-0.0110.0387-0.0208-0.00710.0515-0.02460.025312.2692-36.296627.7741
75.64840.71882.35543.70951.93766.6157-0.0267-0.3211-0.59080.34190.082-0.31550.13660.0159-0.05540.08710.03850.00570.05450.00690.182513.5717-67.114214.5098
82.2364-0.0503-0.04471.89260.59191.8599-0.0298-0.0157-0.08440.0430.0984-0.33190.10170.275-0.06860.02760.0287-0.01860.0492-0.02050.07215.9939-57.219415.0021
96.59551.739-4.09565.9305-1.90012.6701-0.02680.41270.3133-0.62980.22220.08810.1317-0.2731-0.19540.155-0.0177-0.03110.04030.00410.04816.2849-54.43427.7959
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A24 - 45
2X-RAY DIFFRACTION2A46 - 107
3X-RAY DIFFRACTION3A108 - 176
4X-RAY DIFFRACTION4B24 - 45
5X-RAY DIFFRACTION5B46 - 113
6X-RAY DIFFRACTION6B114 - 177
7X-RAY DIFFRACTION7C20 - 45
8X-RAY DIFFRACTION8C46 - 158
9X-RAY DIFFRACTION9C159 - 176

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