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- PDB-3nh6: Nucleotide Binding Domain of human ABCB6 (apo structure) -

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Basic information

Entry
Database: PDB / ID: 3nh6
TitleNucleotide Binding Domain of human ABCB6 (apo structure)
ComponentsATP-binding cassette sub-family B member 6, mitochondrial
KeywordsTRANSPORT PROTEIN / ABC-transporter / ABCB6 / Nucleotide Binding Domain / heme biosynthesis
Function / homology
Function and homology information


Defective ABCB6 causes MCOPCB7 / cellular detoxification of cadmium ion / Mitochondrial ABC transporters / tetrapyrrole metabolic process / ABC-type heme transporter / porphyrin-containing compound metabolic process / tetrapyrrole binding / heme metabolic process / heme transport / porphyrin-containing compound biosynthetic process ...Defective ABCB6 causes MCOPCB7 / cellular detoxification of cadmium ion / Mitochondrial ABC transporters / tetrapyrrole metabolic process / ABC-type heme transporter / porphyrin-containing compound metabolic process / tetrapyrrole binding / heme metabolic process / heme transport / porphyrin-containing compound biosynthetic process / melanosome assembly / heme transmembrane transport / ABC-type heme transporter activity / melanosome membrane / multivesicular body membrane / endolysosome membrane / mitochondrial envelope / vacuolar membrane / skin development / efflux transmembrane transporter activity / intracellular copper ion homeostasis / ABC-type transporter activity / ATP-binding cassette (ABC) transporter complex / brain development / transmembrane transport / early endosome membrane / intracellular iron ion homeostasis / mitochondrial outer membrane / endosome / lysosomal membrane / Golgi membrane / heme binding / endoplasmic reticulum membrane / Golgi apparatus / endoplasmic reticulum / ATP hydrolysis activity / mitochondrion / extracellular exosome / nucleoplasm / ATP binding / plasma membrane / cytosol
Similarity search - Function
Mitochondrial ABC-transporter, N-terminal five TM domain / Mitochondrial ABC-transporter N-terminal five TM region / Type 1 protein exporter / ABC transporter transmembrane region / ABC transporter type 1, transmembrane domain / ABC transporter integral membrane type-1 fused domain profile. / ABC transporter type 1, transmembrane domain superfamily / ABC transporter-like, conserved site / ABC transporters family signature. / ABC transporter ...Mitochondrial ABC-transporter, N-terminal five TM domain / Mitochondrial ABC-transporter N-terminal five TM region / Type 1 protein exporter / ABC transporter transmembrane region / ABC transporter type 1, transmembrane domain / ABC transporter integral membrane type-1 fused domain profile. / ABC transporter type 1, transmembrane domain superfamily / 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. / P-loop containing nucleotide triphosphate hydrolases / ATPases associated with a variety of cellular activities / AAA+ ATPase domain / Rossmann fold / P-loop containing nucleoside triphosphate hydrolase / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
BETA-MERCAPTOETHANOL / ATP-binding cassette sub-family B member 6
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2 Å
AuthorsHaffke, M. / Menzel, A. / Carius, Y. / Jahn, D. / Heinz, D.W.
CitationJournal: Acta Crystallogr.,Sect.D / Year: 2010
Title: Structures of the nucleotide-binding domain of the human ABCB6 transporter and its complexes with nucleotides.
Authors: Haffke, M. / Menzel, A. / Carius, Y. / Jahn, D. / Heinz, D.W.
History
DepositionJun 14, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 25, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Mar 21, 2012Group: Database references
Revision 1.3Sep 6, 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 / 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_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-binding cassette sub-family B member 6, mitochondrial
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,6443
Polymers33,4881
Non-polymers1562
Water2,504139
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)57.229, 68.609, 76.537
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein ATP-binding cassette sub-family B member 6, mitochondrial / Mitochondrial ABC transporter 3 / Mt-ABC transporter 3 / Ubiquitously-expressed mammalian ABC half ...Mitochondrial ABC transporter 3 / Mt-ABC transporter 3 / Ubiquitously-expressed mammalian ABC half transporter / P-glycoprotein-related protein


Mass: 33487.766 Da / Num. of mol.: 1 / Fragment: Nucleotide Binding Domain (UNP residues 558-842)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: ABCB6, MTABC3, PRP, UMAT / Plasmid: pET28 / Production host: Escherichia coli (E. coli) / Strain (production host): Tuner (DE3) / References: UniProt: Q9NP58
#2: Chemical ChemComp-BME / BETA-MERCAPTOETHANOL


Mass: 78.133 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6OS
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 139 / 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: 2.24 Å3/Da / Density % sol: 45.17 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 0.1M MES pH 6.5, 40% (v/v) PEG400, vapor diffusion, hanging drop, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-1 / Wavelength: 0.934 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Sep 17, 2009
RadiationMonochromator: Diamond (111), Ge(220) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.934 Å / Relative weight: 1
ReflectionResolution: 2→33.4 Å / Num. all: 20985 / Num. obs: 20977 / % possible obs: 99.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 15.1 % / Biso Wilson estimate: 39.675 Å2 / Rmerge(I) obs: 0.058 / Net I/σ(I): 37.1
Reflection shellResolution: 2→2.15 Å / Redundancy: 12.2 % / Mean I/σ(I) obs: 5.2 / Num. unique all: 4013 / % possible all: 100

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Phasing

PhasingMethod: molecular replacement
Phasing MR
Highest resolutionLowest resolution
Rotation2.23 Å34.31 Å
Translation2.23 Å34.31 Å

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Processing

Software
NameVersionClassificationNB
MOLREPphasing
REFMACrefinement
PDB_EXTRACT3.1data extraction
DNAdata collection
XDSdata reduction
XSCALEdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2GHI

2ghi


Resolution: 2→31.3 Å / Cor.coef. Fo:Fc: 0.965 / Cor.coef. Fo:Fc free: 0.941 / WRfactor Rfree: 0.212 / WRfactor Rwork: 0.164 / Occupancy max: 1 / Occupancy min: 0.5 / FOM work R set: 0.851 / SU B: 9.492 / SU ML: 0.117 / SU R Cruickshank DPI: 0.169 / SU Rfree: 0.165 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): -3 / ESU R Free: 0.165 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES: WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.239 1049 5 %RANDOM
Rwork0.18 ---
obs0.182 20970 100 %-
all-20985 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso max: 101.22 Å2 / Biso mean: 40.407 Å2 / Biso min: 15.13 Å2
Baniso -1Baniso -2Baniso -3
1--2.56 Å20 Å20 Å2
2--2.06 Å20 Å2
3---0.5 Å2
Refinement stepCycle: LAST / Resolution: 2→31.3 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2091 0 8 139 2238
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0170.0222197
X-RAY DIFFRACTIONr_angle_refined_deg1.5121.9592978
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.6935293
X-RAY DIFFRACTIONr_dihedral_angle_2_deg39.25323.398103
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.42515391
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.7121523
X-RAY DIFFRACTIONr_chiral_restr0.1150.2344
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0211663
X-RAY DIFFRACTIONr_mcbond_it0.8421.51381
X-RAY DIFFRACTIONr_mcangle_it1.4722228
X-RAY DIFFRACTIONr_scbond_it2.4943816
X-RAY DIFFRACTIONr_scangle_it4.0974.5740
LS refinement shellResolution: 2→2.052 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.379 76 -
Rwork0.248 1444 -
all-1520 -
obs-1520 100 %
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)
112.48847.1161-2.24617.4603-3.17416.02260.3004-0.7733-0.20710.8802-0.4174-0.53780.11270.34220.1170.06480.0195-0.04440.1895-0.04320.0751-8.118513.3873-32.3758
23.57890.1128-0.61892.64310.68254.5781-0.07830.53670.2782-0.3311-0.1061-0.0409-0.4130.03310.18440.07790.0015-0.03130.13560.07740.1044-7.1864-9.9858-17.2433
311.31113.06221.386.43550.63954.3691-0.55490.7241-0.229-0.51260.4653-0.1731-0.14990.00880.08950.2052-0.1047-0.01690.1831-0.12410.157-27.3475-29.9333-22.6729
44.33040.68760.15180.8673-0.34863.3769-0.0531-0.2132-0.43290.06950.0094-0.04760.3089-0.09440.04370.05410.01920.02040.06770.04650.1323-12.7162-20.2031-2.0233
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A555 - 572
2X-RAY DIFFRACTION2A573 - 672
3X-RAY DIFFRACTION3A673 - 742
4X-RAY DIFFRACTION4A743 - 828

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