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- PDB-6cum: Crystal structure of a C-terminal proteolytic fragment of a prote... -

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Basic information

Entry
Database: PDB / ID: 6cum
TitleCrystal structure of a C-terminal proteolytic fragment of a protein annotated as an LAO/AO transport system ATPase but likely MeaB and MMAA-like GTPase from Mycobacterium smegmatis
ComponentsLAO/AO transport system ATPase
KeywordsTRANSFERASE / SSGCID / proteolytic fragment / Structural Genomics / Seattle Structural Genomics Center for Infectious Disease
Function / homology
Function and homology information


Transferases; Transferring phosphorus-containing groups / transferase activity / GTPase activity / GTP binding / ATP hydrolysis activity
Similarity search - Function
: / SIMIBI class G3E GTPase, ArgK/MeaB / Methylmalonyl Co-A mutase-associated GTPase MeaB / ATPases associated with a variety of cellular activities / AAA+ ATPase domain / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
LAO/AO transport system ATPase
Similarity search - Component
Biological speciesMycobacterium smegmatis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.6 Å
AuthorsSeattle Structural Genomics Center for Infectious Disease (SSGCID)
CitationJournal: Acta Crystallogr F Struct Biol Commun / Year: 2018
Title: Ab initio structure solution of a proteolytic fragment using ARCIMBOLDO.
Authors: Abendroth, J. / Sankaran, B. / Myler, P.J. / Lorimer, D.D. / Edwards, T.E.
History
DepositionMar 26, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 11, 2018Provider: repository / Type: Initial release
Revision 1.1Sep 12, 2018Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp / citation ...chem_comp / citation / citation_author / entity / pdbx_entity_nonpoly
Item: _chem_comp.name / _citation.country ..._chem_comp.name / _citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.pdbx_database_id_DOI / _citation.title / _citation.year / _entity.pdbx_description / _pdbx_entity_nonpoly.name
Revision 1.2Sep 26, 2018Group: Data collection / Database references / Category: citation
Item: _citation.journal_abbrev / _citation.page_first ..._citation.journal_abbrev / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.3Mar 13, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.4Apr 3, 2024Group: Refinement description / Category: pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: LAO/AO transport system ATPase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,7913
Polymers32,6671
Non-polymers1242
Water1,33374
1
A: LAO/AO transport system ATPase
hetero molecules

A: LAO/AO transport system ATPase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)65,5836
Polymers65,3342
Non-polymers2484
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_555y,x,-z1
Buried area3470 Å2
ΔGint-12 kcal/mol
Surface area6150 Å2
Unit cell
Length a, b, c (Å)48.530, 48.530, 54.820
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number152
Space group name H-MP3121

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Components

#1: Protein LAO/AO transport system ATPase


Mass: 32667.145 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium smegmatis (strain ATCC 700084 / mc(2)155) (bacteria)
Strain: ATCC 700084 / mc(2)155 / Gene: MSMEG_4869 / Plasmid: MysmA.00200.a.A1
Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
Strain (production host): BL21(DE3)
References: UniProt: A0R1T8, Transferases; Transferring phosphorus-containing groups
#2: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6O2
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 74 / 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: 3.01 Å3/Da / Density % sol: 59 %
Crystal growTemperature: 290 K / Method: vapor diffusion, sitting drop / pH: 7
Details: RigakuReagents JCSG+ screen, condition G7: 15% PEG 3350, 100mM succinic acid / NaOH pH 7.0: MysmA.00200.a.A1.PS00535 at 60.5mg/ml: cryo: 25% EG: tray: 215267 G7: puck DZB0-10: no protease was intentionally added

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.2 / Wavelength: 0.9999 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jul 10, 2010
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9999 Å / Relative weight: 1
ReflectionResolution: 1.6→19.622 Å / Num. obs: 10171 / % possible obs: 99.1 % / Redundancy: 4.624 % / Biso Wilson estimate: 22.03 Å2 / CC1/2: 1 / Rmerge(I) obs: 0.033 / Rrim(I) all: 0.037 / Χ2: 0.959 / Net I/σ(I): 24.59
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique obsCC1/2Rrim(I) all% possible all
1.6-1.644.6810.4682.757620.9370.52799.7
1.64-1.694.6390.3283.857170.9830.3799.9
1.69-1.744.6680.2864.326960.9850.32299.9
1.74-1.794.720.2215.297000.9880.249100
1.79-1.854.710.186.766450.9920.20299.4
1.85-1.914.6640.1527.796420.9960.17299.4
1.91-1.984.7440.09412.666130.9970.10699.2
1.98-2.074.6740.07515.686010.9980.08599.8
2.07-2.164.690.05322.235810.9980.059100
2.16-2.264.5060.0428.55510.9990.04599.3
2.26-2.394.4890.04130.715090.9990.04695.9
2.39-2.534.6470.03237.384960.9990.03599.2
2.53-2.74.6370.02742.244800.9990.03100
2.7-2.924.6090.02547.74350.9990.028100
2.92-3.24.4570.02353.264050.9990.02698.8
3.2-3.584.4440.0260.043780.9990.02299.2
3.58-4.134.6140.01868.273320.9990.0299.7
4.13-5.064.5970.01967.962830.9990.02198.3
5.06-7.164.5070.01862.82250.9990.0297
7.16-19.6223.9920.01866.081200.9990.02181.6

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Processing

Software
NameVersionClassification
XDSdata reduction
XSCALEdata scaling
PHENIX(dev_3063)refinement
PDB_EXTRACT3.24data extraction
Arcimboldophasing
PHASERphasing
ARP/wARPmodel building
Cootmodel building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2x 10-residue helices via Acrimboldo

Resolution: 1.6→19.622 Å / SU ML: 0.12 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 22.9
RfactorNum. reflection% reflection
Rfree0.208 979 9.69 %
Rwork0.1744 --
obs0.1774 10103 98.7 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 70.11 Å2 / Biso mean: 32.4202 Å2 / Biso min: 18.98 Å2
Refinement stepCycle: final / Resolution: 1.6→19.622 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms384 0 8 75 467
Biso mean--40.63 44.79 -
Num. residues----51
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 7

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.6001-1.68440.27151390.24311288142799
1.6844-1.78990.27751470.21631278142599
1.7899-1.92790.23671620.20631257141999
1.9279-2.12170.22591140.1761304141899
2.1217-2.42830.19991440.17291292143698
2.4283-3.05750.22671470.163713211468100
3.0575-19.62330.17671260.16531384151098
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)
15.5794-0.65981.68864.4519-1.86365.58070.08540.12390.2140.04-0.3349-0.6668-0.22610.60670.31520.2-0.05460.04460.21610.0090.208925.135218.73170.009
24.4414-2.2477-0.05033.2082-0.22223.7180.04650.1424-0.0722-0.0579-0.0810.1543-0.0031-0.22990.04230.1894-0.0133-0.01180.1925-0.00210.14930.931723.19330.4422
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 240 through 262 )A240 - 262
2X-RAY DIFFRACTION2chain 'A' and (resid 263 through 290 )A263 - 290

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