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- PDB-4q4l: Crystal structure of an ATP synthase subunit beta 1 (F1-B1) from ... -

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Basic information

Entry
Database: PDB / ID: 4q4l
TitleCrystal structure of an ATP synthase subunit beta 1 (F1-B1) from Burkholderia thailandensis
ComponentsATP synthase subunit beta 1
KeywordsHYDROLASE / Structural Genomics / NIAID / National Institute of Allergy and Infectious Diseases / Seattle Structural Genomics Center for Infectious Disease / SSGCID / ATP-binding / metal ion binding / heterooligomeric protein complex / multidomain protein
Function / homology
Function and homology information


proton-transporting ATP synthase complex, catalytic core F(1) / H+-transporting two-sector ATPase / proton-transporting ATPase activity, rotational mechanism / proton-transporting ATP synthase activity, rotational mechanism / ATP binding / plasma membrane
Similarity search - Function
Thrombin, subunit H - #170 / Bovine Mitochondrial F1-ATPase, ATP Synthase Beta Chain; Chain D, domain3 / Bovine Mitochondrial F1-atpase; Atp Synthase Beta Chain; Chain D, domain 3 / ATP synthase, F1 complex, beta subunit / ATPase, F1/V1 complex, beta/alpha subunit, C-terminal / ATPase, F1/V1/A1 complex, alpha/beta subunit, N-terminal domain superfamily / ATPase, F1/V1/A1 complex, alpha/beta subunit, N-terminal domain / ATP synthase alpha/beta family, beta-barrel domain / ATPase, alpha/beta subunit, nucleotide-binding domain, active site / ATP synthase alpha and beta subunits signature. ...Thrombin, subunit H - #170 / Bovine Mitochondrial F1-ATPase, ATP Synthase Beta Chain; Chain D, domain3 / Bovine Mitochondrial F1-atpase; Atp Synthase Beta Chain; Chain D, domain 3 / ATP synthase, F1 complex, beta subunit / ATPase, F1/V1 complex, beta/alpha subunit, C-terminal / ATPase, F1/V1/A1 complex, alpha/beta subunit, N-terminal domain superfamily / ATPase, F1/V1/A1 complex, alpha/beta subunit, N-terminal domain / ATP synthase alpha/beta family, beta-barrel domain / ATPase, alpha/beta subunit, nucleotide-binding domain, active site / ATP synthase alpha and beta subunits signature. / ATPase, F1/V1/A1 complex, alpha/beta subunit, nucleotide-binding domain / ATP synthase alpha/beta family, nucleotide-binding domain / Thrombin, subunit H / P-loop containing nucleotide triphosphate hydrolases / ATPases associated with a variety of cellular activities / AAA+ ATPase domain / Beta Barrel / P-loop containing nucleoside triphosphate hydrolase / Rossmann fold / Orthogonal Bundle / 3-Layer(aba) Sandwich / Mainly Beta / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
ATP synthase subunit beta 1
Similarity search - Component
Biological speciesBurkholderia thailandensis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.2 Å
AuthorsSeattle Structural Genomics Center for Infectious Disease / Seattle Structural Genomics Center for Infectious Disease (SSGCID)
CitationJournal: TO BE PUBLISHED
Title: Crystal structure of an ATP synthase subunit beta 1 (F1-B1) from Burkholderia thailandensis
Authors: Edwards, T.E. / Abendroth, J. / Seattle Structural Genomics Center for Infectious Disease
History
DepositionApr 14, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 30, 2014Provider: repository / Type: Initial release
Revision 1.1Sep 20, 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 / 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 / _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_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_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _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_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_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: ATP synthase subunit beta 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)52,9932
Polymers52,9701
Non-polymers231
Water1,982110
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)45.420, 97.990, 127.540
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein ATP synthase subunit beta 1 / / ATP synthase F1 sector subunit beta 1 / F-ATPase subunit beta 1


Mass: 52970.324 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Burkholderia thailandensis (bacteria) / Strain: E264 / Gene: aptD1, atpD1, BTH_I3308 / Production host: Escherichia coli (E. coli)
References: UniProt: Q2STE9, H+-transporting two-sector ATPase
#2: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 110 / 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: 2.68 Å3/Da / Density % sol: 54.09 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 8
Details: ButhA.17369.c.A1.PW35952 at 19.9 mg/mL with 1 mM MnCl2 and 1 mM ATPgS against PACT screen condition B5, 0.1 M MIB buffer pH 8.0, 25% PEG 1500 with 20% ethylene glycol as cryo-protectant, ...Details: ButhA.17369.c.A1.PW35952 at 19.9 mg/mL with 1 mM MnCl2 and 1 mM ATPgS against PACT screen condition B5, 0.1 M MIB buffer pH 8.0, 25% PEG 1500 with 20% ethylene glycol as cryo-protectant, crystal tracking ID 242856b5, unique tracking ID ppm0-6, 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: 0.97856 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Apr 9, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97856 Å / Relative weight: 1
ReflectionResolution: 2.2→50 Å / Num. all: 29798 / Num. obs: 29756 / % possible obs: 99.9 % / Observed criterion σ(I): -3 / Redundancy: 6 % / Biso Wilson estimate: 50.869 Å2 / Rmerge(I) obs: 0.045 / Χ2: 0.975 / Net I/σ(I): 22.69
Reflection shell

Diffraction-ID: 1

Resolution (Å)Highest resolution (Å)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. unique obs% possible all
2.2-2.260.5413.4913285216199.9
2.26-2.320.4324.33128112085100
2.32-2.390.3475.32128762089100
2.39-2.460.2686.74121761984100
2.46-2.540.2327.7311842192499.9
2.54-2.630.1791011531187899.9
2.63-2.730.14711.8811136181199.9
2.73-2.840.11814.3110880177399.9
2.84-2.970.08818.1310166165899.9
2.97-3.110.06822.549803160699.9
3.11-3.280.05328.129434154899.9
3.28-3.480.04134.158814145799.9
3.48-3.720.03341.748153136699.9
3.72-4.020.03146.2675511282100
4.02-4.40.02751.5769691195100
4.4-4.920.02554.6762731095100
4.92-5.680.02353.745544968100
5.68-6.960.02354.784615821100
6.96-9.840.0257.63589676100
9.840.01953.4163837993.1

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
XSCALEdata scaling
REFMAC5.8.0069refinement
PDB_EXTRACT3.14data extraction
BALBESphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3oaa

3oaa


Resolution: 2.2→50 Å / Cor.coef. Fo:Fc: 0.957 / Cor.coef. Fo:Fc free: 0.943 / WRfactor Rfree: 0.2327 / WRfactor Rwork: 0.1901 / FOM work R set: 0.8186 / SU B: 11.525 / SU ML: 0.143 / SU R Cruickshank DPI: 0.2048 / SU Rfree: 0.1814 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.205 / ESU R Free: 0.181 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: U VALUES : WITH TLS ADDED HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.2361 1462 4.9 %RANDOM
Rwork0.1939 ---
obs0.1959 29696 99.87 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 123.56 Å2 / Biso mean: 56.812 Å2 / Biso min: 29.23 Å2
Baniso -1Baniso -2Baniso -3
1-2.96 Å2-0 Å20 Å2
2---0.52 Å2-0 Å2
3----2.44 Å2
Refinement stepCycle: LAST / Resolution: 2.2→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3201 0 1 110 3312
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0193268
X-RAY DIFFRACTIONr_bond_other_d0.0010.023114
X-RAY DIFFRACTIONr_angle_refined_deg1.4651.9824440
X-RAY DIFFRACTIONr_angle_other_deg0.80437145
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.8025436
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.80324.206126
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.01315522
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.3911520
X-RAY DIFFRACTIONr_chiral_restr0.0780.2523
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0213738
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02686
X-RAY DIFFRACTIONr_mcbond_it2.4183.9811744
X-RAY DIFFRACTIONr_mcbond_other2.4173.981743
X-RAY DIFFRACTIONr_mcangle_it3.6685.9492174
LS refinement shellResolution: 2.2→2.257 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.275 115 -
Rwork0.248 2040 -
all-2155 -
obs--99.91 %
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)
12.4404-0.5719-1.42313.79710.18033.6856-0.10310.7253-0.3274-0.0165-0.1022-0.27280.33680.1670.20530.26630.06310.0430.3503-0.11540.136940.889349.7535-3.5219
20.9751-1.0608-0.40532.74991.02061.13490.03460.01350.0135-0.06850.0581-0.39320.08210.1492-0.09270.16820.02310.04450.0255-0.00740.099134.225568.094915.8906
30.5322-0.6901-0.33273.0630.98021.4244-0.016-0.05090.2010.09880.1338-0.4226-0.1630.11-0.11780.1412-0.0186-0.00140.0118-0.02370.093828.033992.416426.9923
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A18 - 92
2X-RAY DIFFRACTION2A93 - 298
3X-RAY DIFFRACTION3A299 - 476

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