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- PDB-4pfs: Crystal Structure of Cobyrinic Acid a,c-diamide synthase from Myc... -

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Basic information

Entry
Database: PDB / ID: 4pfs
TitleCrystal Structure of Cobyrinic Acid a,c-diamide synthase from Mycobacterium smegmatis
ComponentsCobyrinic Acid a,c-diamide synthase
KeywordsLIGASE / SSGCID / COBYRINIC ACID A / C-DIAMIDE SYNTHASE / Structural Genomics / Seattle Structural Genomics Center for Infectious Disease
Function / homology
Function and homology information


nucleotide binding / metal ion binding
Similarity search - Function
AAA domain / AAA domain / P-loop containing nucleotide triphosphate hydrolases / P-loop containing nucleoside triphosphate hydrolase / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Cobyrinic Acid a,c-diamide synthase
Similarity search - Component
Biological speciesMycobacterium smegmatis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å
AuthorsSeattle Structural Genomics Center for Infectious Disease (SSGCID)
CitationJournal: TO BE PUBLISHED
Title: Crystal Structure of Cobyrinic Acid a,c-diamide synthase from Mycobacterium smegmatis
Authors: Davies, D.R. / Fairman, J. / Abendroth, J.
History
DepositionApr 30, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 21, 2014Provider: repository / Type: Initial release
Revision 1.1Feb 4, 2015Group: Derived calculations
Revision 1.2Nov 22, 2017Group: Database references / Derived calculations ...Database references / Derived calculations / Other / Refinement description / Source and taxonomy / Structure summary
Category: citation / entity_src_gen ...citation / entity_src_gen / pdbx_database_status / pdbx_struct_assembly / pdbx_struct_oper_list / software / struct_keywords
Item: _citation.journal_id_CSD / _entity_src_gen.pdbx_alt_source_flag ..._citation.journal_id_CSD / _entity_src_gen.pdbx_alt_source_flag / _pdbx_database_status.pdb_format_compatible / _pdbx_struct_assembly.oligomeric_details / _pdbx_struct_oper_list.symmetry_operation / _software.classification / _struct_keywords.text
Revision 1.3Sep 27, 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 / refine_hist
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Cobyrinic Acid a,c-diamide synthase
B: Cobyrinic Acid a,c-diamide synthase


Theoretical massNumber of molelcules
Total (without water)58,8222
Polymers58,8222
Non-polymers00
Water2,090116
1
A: Cobyrinic Acid a,c-diamide synthase


Theoretical massNumber of molelcules
Total (without water)29,4111
Polymers29,4111
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Cobyrinic Acid a,c-diamide synthase


Theoretical massNumber of molelcules
Total (without water)29,4111
Polymers29,4111
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)88.810, 88.810, 122.310
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212

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Components

#1: Protein Cobyrinic Acid a,c-diamide synthase


Mass: 29410.924 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium smegmatis (bacteria) / Strain: ATCC 700084 / Gene: MSMEG_1927 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: A0QTQ5
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 116 / 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: 2.05 Å3/Da / Density % sol: 40 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 8
Details: EBS INTERNAL TRACKING NUMBER 500 MM NACL, 2 MM DTT, 0.025% SODIUM AZIDE, 5% GLYCEROL, 0.4 100 MM TRIS PH 8.0; 10% MPD ADDED AS CRYOPROTECTANT, VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 289K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-G / Wavelength: 0.9786 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Feb 27, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9786 Å / Relative weight: 1
ReflectionResolution: 2.3→80 Å / Num. obs: 22458 / % possible obs: 99.9 % / Observed criterion σ(I): -3 / Redundancy: 9.6 % / Biso Wilson estimate: 40.61 Å2 / Rmerge(I) obs: 0.088 / Net I/σ(I): 19.92
Reflection shellResolution: 2.3→2.36 Å / Rmerge(I) obs: 0.515 / Mean I/σ(I) obs: 4.5 / % possible all: 100

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Processing

Software
NameVersionClassification
BALBESphasing
PHENIX(PHENIX.REFINE: 1.9_1675)refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1WCV

1wcv


Resolution: 2.3→39.72 Å / Cross valid method: FREE R-VALUE / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.231 1046 4.82 %
Rwork0.168 --
obs0.171 22458 99.9 %
Solvent computationShrinkage radii: 0.9 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 37.21 Å2
Refinement stepCycle: LAST / Resolution: 2.3→39.72 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3567 0 0 116 3683
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)
13.3673-0.2841.69752.1246-0.37954.308-0.0306-0.36180.0490.35340.10430.1868-0.2775-0.2859-0.04360.27190.03820.0430.15730.01810.20373.4157-20.5598-18.3676
21.8682-0.4636-0.12231.65680.57030.4281-0.08820.3072-0.4727-0.26670.2638-0.6308-0.32760.7252-0.03130.2811-0.02430.02990.3601-0.04440.36521.0799-21.208-21.9663
33.38280.83790.79551.86391.01013.58280.11190.332-0.25350.1570.13480.02420.35550.453-0.20670.28990.0703-0.03520.1837-0.03790.23926.954-27.6468-30.5189
43.9739-0.24021.73565.253-1.23396.10560.29410.9489-0.0158-0.7442-0.12410.449-0.4675-0.5649-0.16330.30550.062-0.10680.43670.04330.313-7.9629-16.5149-46.4893
50.62930.28130.74752.4998-1.54054.55590.0971-0.1568-0.2172-0.1810.13760.678-0.145-0.2981-0.22270.23220.0438-0.08480.2266-0.00880.2451-7.9022-21.1589-36.9021
62.8650.95131.26021.94620.15055.43890.2851-0.1873-0.4763-0.21690.26380.48880.5985-0.8095-0.40660.3062-0.0978-0.04070.41820.11920.407-11.4265-28.973-31.8565
73.38460.88730.48854.47631.23583.1910.1843-0.00750.0392-0.1392-0.2072-0.5183-0.0340.330.01590.20280.03870.02080.29890.11180.196-4.728918.1814-45.6663
82.4970.46240.12364.24281.66174.03450.1363-0.11120.15330.3422-0.2721-0.47580.04680.21390.03880.2439-0.0692-0.05340.24880.07260.323-2.009625.4399-34.5922
94.68350.9602-0.43534.0511-1.26516.72980.2832-0.0280.2328-0.0054-0.5302-0.782-0.36731.0320.20590.2613-0.0948-0.06740.39760.15620.39132.334827.3164-37.217
103.801-0.20870.45911.73580.25893.23430.0196-0.35210.4180.5141-0.28850.1496-0.8705-0.4042-0.16360.3275-0.00420.05640.2422-0.0370.3389-14.311130.1557-32.9604
113.0784-0.0904-0.00672.18221.55772.88510.04370.05930.05250.0274-0.24120.2560.0308-0.11650.20630.2138-0.0038-0.00950.23740.07080.1702-15.07918.4215-43.9509
123.3115-0.9139-0.91633.92951.92932.0939-0.02210.4168-0.4521-0.432-0.07010.36980.2669-0.04670.18370.3765-0.0101-0.02860.2843-0.01470.2348-13.39356.9028-52.087
138.97690.92591.28864.83661.30012.1946-0.38030.05730.04290.19860.1675-0.4187-0.10120.0580.08430.32960.0419-0.01270.3898-0.0150.2116-6.70798.4621-53.5737
140.65490.76210.45722.45820.82450.4276-0.07990.2331-0.5817-0.5587-0.1426-0.4790.1660.34490.08620.41380.03530.15250.34950.03360.2712-3.918315.8483-58.3107
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 9 through 95 )
2X-RAY DIFFRACTION2chain 'A' and (resid 96 through 110 )
3X-RAY DIFFRACTION3chain 'A' and (resid 111 through 191 )
4X-RAY DIFFRACTION4chain 'A' and (resid 192 through 210 )
5X-RAY DIFFRACTION5chain 'A' and (resid 211 through 242 )
6X-RAY DIFFRACTION6chain 'A' and (resid 243 through 271 )
7X-RAY DIFFRACTION7chain 'B' and (resid 9 through 37 )
8X-RAY DIFFRACTION8chain 'B' and (resid 38 through 77 )
9X-RAY DIFFRACTION9chain 'B' and (resid 78 through 95 )
10X-RAY DIFFRACTION10chain 'B' and (resid 96 through 122 )
11X-RAY DIFFRACTION11chain 'B' and (resid 123 through 178 )
12X-RAY DIFFRACTION12chain 'B' and (resid 179 through 211 )
13X-RAY DIFFRACTION13chain 'B' and (resid 212 through 242 )
14X-RAY DIFFRACTION14chain 'B' and (resid 243 through 271 )

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