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- PDB-4yer: Crystal structure of an ABC transporter ATP-binding protein (TM_1... -

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Basic information

Entry
Database: PDB / ID: 4yer
TitleCrystal structure of an ABC transporter ATP-binding protein (TM_1403) from Thermotoga maritima MSB8 at 2.35 A resolution
ComponentsABC transporter ATP-binding protein
KeywordsHYDROLASE / PF00005 family protein / P-loop containing nucleoside triphosphate hydrolases fold / Structural Genomics / Joint Center for Structural Genomics / JCSG / Protein Structure Initiative / PSI-BIOLOGY
Function / homology
Function and homology information


doxorubicin transport / daunorubicin transport / ATP hydrolysis activity / ATP binding
Similarity search - Function
Daunorubicin resistance ABC transporter ATP-binding subunit DrrA / Domain of unknown function DUF4162 / Domain of unknown function (DUF4162) / ABC transporter-like, conserved site / ABC transporters family signature. / ABC transporter / ABC transporter-like, ATP-binding domain / ATP-binding cassette, ABC transporter-type domain profile. / ATPases associated with a variety of cellular activities / AAA+ ATPase domain / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
ADENOSINE-5'-DIPHOSPHATE / Antibiotic ABC transporter, ATP-binding protein, putative
Similarity search - Component
Biological speciesThermotoga maritima (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / MAD/molecular replacement / Resolution: 2.35 Å
AuthorsJoint Center for Structural Genomics (JCSG)
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM094586 United States
CitationJournal: To be published
Title: Crystal structure of an ABC transporter ATP-binding protein (TM_1403) from Thermotoga maritima MSB8 at 2.35 A resolution
Authors: Joint Center for Structural Genomics (JCSG)
History
DepositionFeb 24, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 11, 2015Provider: repository / Type: Initial release
Revision 1.1Sep 20, 2017Group: Author supporting evidence / Derived calculations ...Author supporting evidence / Derived calculations / Refinement description / Source and taxonomy
Category: entity_src_gen / pdbx_audit_support ...entity_src_gen / pdbx_audit_support / pdbx_struct_oper_list / software
Item: _entity_src_gen.pdbx_alt_source_flag / _pdbx_audit_support.funding_organization / _pdbx_struct_oper_list.symmetry_operation
Revision 1.2Nov 1, 2017Group: Author supporting evidence / Category: pdbx_struct_assembly_auth_evidence
Revision 1.3Jan 24, 2018Group: Database references / Category: citation_author / Item: _citation_author.name
Revision 1.4Dec 25, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.5Feb 1, 2023Group: Database references / Category: database_2 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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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)77,5106
Polymers76,5852
Non-polymers9254
Water1,08160
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4000 Å2
ΔGint-43 kcal/mol
Surface area23670 Å2
MethodPISA
Unit cell
Length a, b, c (Å)61.310, 101.180, 110.210
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
DetailsDimer according to analytical size exclusion

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Components

#1: Protein ABC transporter ATP-binding protein / ABC-type multidrug transport system / ATPase component / Antibiotic ABC transporter / ATP-binding ...ABC-type multidrug transport system / ATPase component / Antibiotic ABC transporter / ATP-binding protein / putative


Mass: 38292.465 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermotoga maritima (bacteria) / Strain: ATCC 43589 / MSB8 / DSM 3109 / JCM 10099 / Gene: TM_1403, THEMA_07300, Tmari_1410 / Plasmid: MH4TEVa / Production host: Escherichia Coli (E. coli) / Strain (production host): HK100 / References: UniProt: Q9X1C3
#2: Chemical ChemComp-ADP / ADENOSINE-5'-DIPHOSPHATE


Mass: 427.201 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H15N5O10P2 / Comment: ADP, energy-carrying molecule*YM
#3: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 60 / 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: 2

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Sample preparation

Crystal
IDDensity Matthews (Å3/Da)Density % sol (%)
12.2344.89
2
Crystal grow
Temperature (K)Crystal-IDMethodpHDetails
2931vapor diffusion, sitting drop4.2854.0% polyethylene glycol 200, 0.2M sodium chloride, 0.1M phosphate-citrate pH 4.28
2932vapor diffusion, sitting drop4.20.2M sodium chloride, 55.0% polyethylene glycol 200, 0.1M phosphate-citrate pH 4.2

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
21001
31001
41001
51001
61002
Diffraction source
SourceSiteBeamlineIDWavelength (Å)
SYNCHROTRONSSRL BL1-510.999974
SYNCHROTRONSSRL BL11-160.97926,0.91837,0.97894
Detector
TypeIDDetectorDateDetails
ADSC QUANTUM 41CCDFeb 22, 20072-crystal monochromator, Si111, 1m long Rh coated bent cylindrical mirror for horizontal and vertical focussing
MARMOSAIC 325 mm CCD6CCDFeb 8, 2007Flat mirror (vertical focusing); single crystal Si(111) bent monochromator (ho rizontal focusing)
Radiation
IDMonochromatorProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
12-crystal, Si111SINGLE WAVELENGTHMx-ray1
6single crystal Si(111) bentMADMx-ray2
Radiation wavelength
IDWavelength (Å)Relative weight
10.9999741
20.979261
30.918371
40.978941
ReflectionResolution: 2.35→29.725 Å / Num. all: 29295 / Num. obs: 29295 / % possible obs: 99.9 % / Redundancy: 4 % / Rpim(I) all: 0.048 / Rrim(I) all: 0.096 / Rsym value: 0.083 / Net I/av σ(I): 6.702 / Net I/σ(I): 10.6 / Num. measured all: 117826
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) allRmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allRpim(I) allRrim(I) allRsym valueDiffraction-IDNet I/σ(I) obs% possible all
2.35-2.414.10.9210.81871221370.4520.9210.811.9100
2.41-2.484.10.7620.6631.2848020690.3730.7620.6632.3100
2.48-2.554.10.5680.4931.6823020170.2790.5680.4933100
2.55-2.634.10.4510.3912802019750.2220.4510.3913.6100
2.63-2.714.10.4090.3552.1777419020.2010.4090.3554100
2.71-2.814.10.3540.3072.5756718520.1740.3540.3074.5100
2.81-2.914.10.2630.2283.3723517770.130.2630.2285.9100
2.91-3.034.10.2120.1844.1697517210.1040.2120.1847.1100
3.03-3.174.10.1730.155.1680516680.0850.1730.158.5100
3.17-3.324.10.1270.116.8638715740.0630.1270.1110.9100
3.32-3.540.0960.0838.5610815200.0480.0960.08313.4100
3.5-3.7240.080.0699.9578014280.040.080.06916.3100
3.72-3.9740.0620.05312.2543913590.0310.0620.05320.3100
3.97-4.2940.0580.04911.4501412580.0290.0580.04921.7100
4.29-4.740.050.04313.5474711830.0250.050.04324.8100
4.7-5.253.90.0510.04413.3415710660.0250.0510.04423.8100
5.25-6.073.90.0580.051237039480.0290.0580.0521.7100
6.07-7.433.80.0580.04910.131068230.030.0580.04922.4100
7.43-10.513.70.0470.0411.223876490.0250.0470.0426.799.7
10.51-29.7253.30.0460.03813.212003690.0240.0460.03824.695.2

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Phasing

PhasingMethod: MAD/molecular replacement

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Processing

Software
NameVersionClassification
PDB_EXTRACT3.1data extraction
SHELXphasing
SHARPphasing
SCALA3.3.20data scaling
BUSTER-TNT2.10.0refinement
XDSdata reduction
SHELXDphasing
BUSTER2.10.0refinement
RefinementMethod to determine structure: MAD / Resolution: 2.35→29.725 Å / Cor.coef. Fo:Fc: 0.9203 / Cor.coef. Fo:Fc free: 0.9126 / Occupancy max: 1 / Occupancy min: 0.75 / Cross valid method: THROUGHOUT / σ(F): 0
Details: 1. ZERO OCCUPANCY HYDROGENS WERE INCLUDED DURING REFINEMENT TO IMPROVE THE ANTI-BUMPING RESTRAINTS. 2. ATOM RECORDS CONTAIN SUM OF TLS AND RESIDUAL B FACTORS. 3. ANISOU RECORDS CONTAIN SUM ...Details: 1. ZERO OCCUPANCY HYDROGENS WERE INCLUDED DURING REFINEMENT TO IMPROVE THE ANTI-BUMPING RESTRAINTS. 2. ATOM RECORDS CONTAIN SUM OF TLS AND RESIDUAL B FACTORS. 3. ANISOU RECORDS CONTAIN SUM OF TLS AND RESIDUAL U FACTORS. 4. A MET-INHIBITION PROTOCOL WAS USED FOR SELENOMETHIONINE INCORPORATION DURING PROTEIN EXPRESSION. THE OCCUPANCY OF THE SE ATOMS IN THE MSE RESIDUES WAS REDUCED TO 0.75 FOR THE REDUCED SCATTERING POWER DUE TO PARTIAL S-MET INCORPORATION. 5. NCS RESTRAINTS WERE APPLIED DURING REFINEMENT USING LSSR (-AUTONCS) IN BUSTER. 6. LIGAND MOLECULES ADENOSINE-5'-DIPHOSPHATE (ADP) ARE MODELED IN EACH CHAIN BASED ON ELECTRON DENSITY AND HOMOLOGOUS STRUCTURES.
RfactorNum. reflection% reflectionSelection details
Rfree0.2416 1481 5.07 %RANDOM
Rwork0.2226 ---
obs0.2236 29234 99.95 %-
Displacement parametersBiso max: 231.38 Å2 / Biso mean: 62.2966 Å2 / Biso min: 24.15 Å2
Baniso -1Baniso -2Baniso -3
1-2.331 Å20 Å20 Å2
2--5.3642 Å20 Å2
3----7.6951 Å2
Refine analyzeLuzzati coordinate error obs: 0.305 Å
Refinement stepCycle: LAST / Resolution: 2.35→29.725 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4310 0 56 60 4426
Refine LS restraints
Refine-IDTypeNumberRestraint functionWeightDev ideal
X-RAY DIFFRACTIONt_dihedral_angle_d2427SINUSOIDAL2
X-RAY DIFFRACTIONt_trig_c_planes95HARMONIC2
X-RAY DIFFRACTIONt_gen_planes1303HARMONIC5
X-RAY DIFFRACTIONt_it8648HARMONIC20
X-RAY DIFFRACTIONt_nbd0SEMIHARMONIC5
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_chiral_improper_torsion606SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact9117SEMIHARMONIC4
X-RAY DIFFRACTIONt_bond_d8648HARMONIC20.009
X-RAY DIFFRACTIONt_angle_deg15665HARMONIC20.96
X-RAY DIFFRACTIONt_omega_torsion3.36
X-RAY DIFFRACTIONt_other_torsion2.95
LS refinement shellResolution: 2.35→2.43 Å / Total num. of bins used: 15
RfactorNum. reflection% reflection
Rfree0.2557 144 5.13 %
Rwork0.2115 2663 -
all0.2138 2807 -
obs--99.95 %
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)
11.9818-0.0670.00711.67930.39621.94140.02030.0559-0.11550.03410.0163-0.15870.2838-0.0083-0.0367-0.2296-0.015-0.0474-0.23590.00630.062811.7363-19.156580.0341
21.842-0.44230.27882.9097-0.94561.06750.0340.0490.2773-0.0199-0.0873-0.1461-0.08830.0050.0533-0.2417-0.00440.0269-0.2205-0.01790.0814-12.0484-30.779780.9971
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1{ A|1-313 }A1 - 313
2X-RAY DIFFRACTION2{ B|1-313 }B1 - 313

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