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- PDB-4dn7: CRYSTAL STRUCTURE OF putative ABC transporter, ATP-binding protei... -

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Basic information

Entry
Database: PDB / ID: 4dn7
TitleCRYSTAL STRUCTURE OF putative ABC transporter, ATP-binding protein from Methanosarcina mazei Go1
ComponentsABC transporter, ATP-binding protein
KeywordsTRANSPORT PROTEIN / STRUCTURAL GENOMICS / PROTEIN STRUCTURE INITIATIVE / NEW YORK STRUCTURAL GENOMIX RESEARCH CONSORTIUM / NYSGRC / PSI-Biology / New York Structural Genomics Research Consortium
Function / homologySUF system FeS cluster assembly, SufBD / SUF system FeS cluster assembly, SufBD superfamily / : / SUF system FeS cluster assembly, SufBD core domain / iron-sulfur cluster assembly / ATP binding / ABC transporter, ATP-binding protein
Function and homology information
Biological speciesMethanosarcina maze (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / MAD / Resolution: 1.6 Å
AuthorsMalashkevich, V.N. / Bhosle, R. / Toro, R. / Seidel, R. / Almo, S.C. / New York Structural Genomics Research Consortium (NYSGRC)
CitationJournal: To be Published
Title: CRYSTAL STRUCTURE OF putative ABC transporter, ATP-binding protein from Methanosarcina mazei Go1
Authors: Malashkevich, V.N. / Bhosle, R. / Toro, R. / Seidel, R. / Almo, S.C.
History
DepositionFeb 8, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 22, 2012Provider: repository / Type: Initial release
Revision 1.1Nov 20, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / struct_conn / 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_conn.pdbx_leaving_atom_flag / _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: ABC transporter, ATP-binding protein
B: ABC transporter, ATP-binding protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)96,1686
Polymers95,2152
Non-polymers9534
Water9,206511
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3760 Å2
ΔGint-18 kcal/mol
Surface area32160 Å2
MethodPISA
Unit cell
Length a, b, c (Å)52.913, 52.879, 88.142
Angle α, β, γ (deg.)106.510, 97.430, 105.910
Int Tables number1
Space group name H-MP1
Detailsbiological unit is the same as asym.

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Components

#1: Protein ABC transporter, ATP-binding protein


Mass: 47607.273 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Methanosarcina maze (archaea) / Strain: Go1 / Gene: MM_1088 / Plasmid: BC-PSGX3(BC) / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)CODON+RIL / References: UniProt: Q8PXX8
#2: Chemical
ChemComp-1PE / PENTAETHYLENE GLYCOL / PEG400


Mass: 238.278 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C10H22O6 / Comment: precipitant*YM
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 511 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 2.33 Å3/Da / Density % sol: 47.14 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 0.1 M Na acetate, 0.1M MES:NaOH, pH 6.5, 30% PEG400, VAPOR DIFFUSION, SITTING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X29A / Wavelength: 0.9791 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Feb 3, 2012
RadiationProtocol: SINGLE WAVELENGTH / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9791 Å / Relative weight: 1
ReflectionRedundancy: 3.8 % / Av σ(I) over netI: 27.02 / Number: 384030 / Rmerge(I) obs: 0.075 / Χ2: 2.06 / D res high: 1.6 Å / D res low: 50 Å / Num. obs: 101227 / % possible obs: 88.9
Diffraction reflection shell
Highest resolution (Å)Lowest resolution (Å)% possible obs (%)IDRmerge(I) obsChi squaredRedundancy
4.345092.710.0599.6443.9
3.454.3460.910.0474.4863.5
3.013.4598.110.0523.6693.8
2.743.0198.310.0623.1183.9
2.542.7498.210.0712.5063.9
2.392.5497.910.0792.0423.9
2.272.3990.810.0961.8333.8
2.172.2756.110.1171.6083.7
2.092.1797.210.1171.3773.9
2.022.099710.1351.3333.9
1.952.0296.810.1911.2713.9
1.91.9535.210.2821.4533.3
1.851.99510.3551.0493.8
1.81.8596.210.3810.9473.9
1.761.895.910.4660.8953.9
1.721.7695.910.5510.8673.9
1.691.7295.810.7230.8543.9
1.661.6995.310.7980.8313.8
1.631.6694.210.8770.8173.5
1.61.639010.8950.8153.2
ReflectionResolution: 1.6→50 Å / Num. obs: 101227 / % possible obs: 88.9 % / Redundancy: 3.8 % / Rmerge(I) obs: 0.075 / Χ2: 2.062 / Net I/σ(I): 9.4
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
1.6-1.633.20.89550730.815190
1.63-1.663.50.87754150.817194.2
1.66-1.693.80.79853790.831195.3
1.69-1.723.90.72354730.854195.8
1.72-1.763.90.55154890.867195.9
1.76-1.83.90.46654050.895195.9
1.8-1.853.90.38154870.947196.2
1.85-1.93.80.35554511.049195
1.9-1.953.30.28220001.453135.2
1.95-2.023.90.19155061.271196.8
2.02-2.093.90.13555161.333197
2.09-2.173.90.11755311.377197.2
2.17-2.273.70.11731911.608156.1
2.27-2.393.80.09651911.833190.8
2.39-2.543.90.07955992.042197.9
2.54-2.743.90.07155712.506198.2
2.74-3.013.90.06255943.118198.3
3.01-3.453.80.05255963.669198.1
3.45-4.343.50.04734744.486160.9
4.34-503.90.05952869.644192.7

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Phasing

PhasingMethod: MAD

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Processing

Software
NameVersionClassificationNB
SCALEPACKdata scaling
SHELXphasing
REFMACrefinement
PDB_EXTRACT3.1data extraction
CBASSdata collection
HKL-2000data reduction
SHELXDphasing
RefinementMethod to determine structure: SAD / Resolution: 1.6→19.56 Å / Cor.coef. Fo:Fc: 0.972 / Cor.coef. Fo:Fc free: 0.947 / WRfactor Rfree: 0.2268 / WRfactor Rwork: 0.1669 / Occupancy max: 1 / Occupancy min: 0.5 / FOM work R set: 0.821 / SU B: 4.799 / SU ML: 0.073 / SU R Cruickshank DPI: 0.1247 / SU Rfree: 0.1048 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.125 / ESU R Free: 0.105 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT U VALUES : RESIDUAL ONLY
RfactorNum. reflection% reflectionSelection details
Rfree0.232 5014 5 %RANDOM
Rwork0.1657 ---
obs0.169 100625 88.84 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 85.93 Å2 / Biso mean: 29.2047 Å2 / Biso min: 14.54 Å2
Baniso -1Baniso -2Baniso -3
1--0.01 Å20.05 Å2-0.04 Å2
2--0.12 Å20.09 Å2
3----0.04 Å2
Refinement stepCycle: LAST / Resolution: 1.6→19.56 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6213 0 38 511 6762
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0196378
X-RAY DIFFRACTIONr_angle_refined_deg1.3191.9948599
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.6715826
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.46825.426258
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.824151150
X-RAY DIFFRACTIONr_dihedral_angle_4_deg9.8421530
X-RAY DIFFRACTIONr_chiral_restr0.0850.2999
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0214628
X-RAY DIFFRACTIONr_rigid_bond_restr2.96436378
X-RAY DIFFRACTIONr_sphericity_free25.1165191
X-RAY DIFFRACTIONr_sphericity_bonded14.73956610
LS refinement shellResolution: 1.6→1.641 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.338 372 -
Rwork0.263 7231 -
all-7603 -
obs--91.51 %
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)
10.3195-0.045-0.04330.1780.04880.25770.0071-0.0578-0.01830.0483-0.0089-0.00040.00830.02190.00180.0176-0.01090.0070.0197-0.00790.022530.66774.266511.581
20.2407-0.0859-0.02960.3802-0.03850.29540.00270.049-0.0101-0.0746-0.01070.0195-0.0006-0.00950.00790.02-0.00590.00570.0165-0.01360.023325.27658.8227-31.8379
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A-10 - 9999
2X-RAY DIFFRACTION2B-10 - 9999

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