[English] 日本語
Yorodumi
- PDB-3puz: Crystal Structure of a pre-translocation state MBP-Maltose transp... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 3puz
TitleCrystal Structure of a pre-translocation state MBP-Maltose transporter complex bound to AMP-PNP
Components
  • (Maltose transporter subunit; membrane component of ABC ...) x 2
  • Fused maltose transport subunit, ATP-binding component of ABC superfamily; regulatory protein
  • Maltose transporter subunit; periplasmic-binding component of ABC superfamily
KeywordsTRANSPORT PROTEIN / MEMBRANE PROTEIN / ATP Binding Cassette / Nucleotide Binding Domain / Substrate Binding Protein / ABC Transporter / importer / ATPase / ATP binding / Maltodextrin binding / transmembrane integral membrane
Function / homology
Function and homology information


ABC-type maltose transporter / ABC-type maltose transporter activity / negative regulation of maltose transport / enzyme IIA-maltose transporter complex / negative regulation of transmembrane transport / detection of maltose stimulus / maltose binding / maltose transport complex / maltose transport / maltodextrin transmembrane transport ...ABC-type maltose transporter / ABC-type maltose transporter activity / negative regulation of maltose transport / enzyme IIA-maltose transporter complex / negative regulation of transmembrane transport / detection of maltose stimulus / maltose binding / maltose transport complex / maltose transport / maltodextrin transmembrane transport / carbohydrate transmembrane transporter activity / ATP-binding cassette (ABC) transporter complex, substrate-binding subunit-containing / carbohydrate transport / ATP-binding cassette (ABC) transporter complex / cell chemotaxis / outer membrane-bounded periplasmic space / DNA-binding transcription factor binding / periplasmic space / DNA damage response / ATP hydrolysis activity / ATP binding / membrane / plasma membrane
Similarity search - Function
MalF N-terminal region-like / Periplasmic binding protein-like II / D-maltodextrin-binding protein, MBP / MalF N-terminal region-like / MalF N-terminal region-like / Maltose transport system permease protein MalF, P2 domain / MalF, N-terminal / : / : / Maltose transport system permease protein MalF P2 domain ...MalF N-terminal region-like / Periplasmic binding protein-like II / D-maltodextrin-binding protein, MBP / MalF N-terminal region-like / MalF N-terminal region-like / Maltose transport system permease protein MalF, P2 domain / MalF, N-terminal / : / : / Maltose transport system permease protein MalF P2 domain / MalF, N-terminal region, transmembrane helices / MetI-like fold / MetI-like / Maltose/Maltodextrin import ATP-binding protein malK family profile. / Transport-associated OB, type 2 / TOBE domain / MalK OB fold domain / ABC transporter, maltose/maltodextrin import, MalK-like / : / Molybdate/tungstate binding, C-terminal / ABC transporter type 1, transmembrane domain MetI-like / MetI-like superfamily / Binding-protein-dependent transport system inner membrane component / ABC transporter integral membrane type-1 domain profile. / RNA polymerase II/Efflux pump adaptor protein, barrel-sandwich hybrid domain / Maltose/Cyclodextrin ABC transporter, substrate-binding protein / Solute-binding family 1, conserved site / Bacterial extracellular solute-binding proteins, family 1 signature. / Bacterial extracellular solute-binding protein / Bacterial extracellular solute-binding protein / Nucleic acid-binding proteins / Methane Monooxygenase Hydroxylase; Chain G, domain 1 / ABC transporter-like, conserved site / ABC transporters family signature. / Periplasmic binding protein-like II / ABC transporter / ABC transporter-like, ATP-binding domain / ATP-binding cassette, ABC transporter-type domain profile. / D-Maltodextrin-Binding Protein; domain 2 / OB fold (Dihydrolipoamide Acetyltransferase, E2P) / P-loop containing nucleotide triphosphate hydrolases / ATPases associated with a variety of cellular activities / AAA+ ATPase domain / Nucleic acid-binding, OB-fold / Roll / Up-down Bundle / 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
alpha-maltose / PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER / Chem-PGV / : / : / : / : / Maltose/maltodextrin transport system permease protein MalF / Maltose/maltodextrin-binding periplasmic protein / Maltose/maltodextrin transport system permease protein MalG / Maltose/maltodextrin import ATP-binding protein MalK
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.9 Å
AuthorsOldham, M.L. / Chen, J.
CitationJournal: Science / Year: 2011
Title: Crystal structure of the maltose transporter in a pretranslocation intermediate state.
Authors: Oldham, M.L. / Chen, J.
History
DepositionDec 6, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 18, 2011Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 2.0Jul 29, 2020Group: Atomic model / Data collection ...Atomic model / Data collection / Database references / Derived calculations / Non-polymer description / Structure summary
Category: atom_site / atom_site_anisotrop ...atom_site / atom_site_anisotrop / chem_comp / entity / entity_name_com / pdbx_branch_scheme / pdbx_chem_comp_identifier / pdbx_entity_branch / pdbx_entity_branch_descriptor / pdbx_entity_branch_link / pdbx_entity_branch_list / pdbx_entity_nonpoly / pdbx_molecule_features / pdbx_nonpoly_scheme / struct_conn / struct_conn_type / struct_ref_seq_dif / struct_site / struct_site_gen
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_asym_id / _atom_site.auth_atom_id / _atom_site.auth_comp_id / _atom_site.auth_seq_id / _atom_site.label_atom_id / _atom_site.label_comp_id / _atom_site_anisotrop.U[1][1] / _atom_site_anisotrop.U[1][2] / _atom_site_anisotrop.U[1][3] / _atom_site_anisotrop.U[2][2] / _atom_site_anisotrop.U[2][3] / _atom_site_anisotrop.U[3][3] / _atom_site_anisotrop.pdbx_auth_asym_id / _atom_site_anisotrop.pdbx_auth_atom_id / _atom_site_anisotrop.pdbx_auth_comp_id / _atom_site_anisotrop.pdbx_auth_seq_id / _atom_site_anisotrop.pdbx_label_atom_id / _atom_site_anisotrop.pdbx_label_comp_id / _chem_comp.formula / _chem_comp.formula_weight / _chem_comp.id / _chem_comp.mon_nstd_flag / _chem_comp.name / _chem_comp.pdbx_synonyms / _chem_comp.type / _entity.formula_weight / _entity.pdbx_description / _entity.type / _struct_ref_seq_dif.details
Description: Carbohydrate remediation / Provider: repository / Type: Remediation

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
E: Maltose transporter subunit; periplasmic-binding component of ABC superfamily
F: Maltose transporter subunit; membrane component of ABC superfamily
G: Maltose transporter subunit; membrane component of ABC superfamily
A: Fused maltose transport subunit, ATP-binding component of ABC superfamily; regulatory protein
B: Fused maltose transport subunit, ATP-binding component of ABC superfamily; regulatory protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)216,97812
Polymers214,4845
Non-polymers2,4957
Water1448
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area24320 Å2
ΔGint-179 kcal/mol
Surface area78710 Å2
MethodPISA
Unit cell
Length a, b, c (Å)80.021, 93.360, 119.761
Angle α, β, γ (deg.)90.05, 102.57, 105.01
Int Tables number1
Space group name H-MP1

-
Components

-
Protein , 2 types, 3 molecules EAB

#1: Protein Maltose transporter subunit; periplasmic-binding component of ABC superfamily


Mass: 40815.305 Da / Num. of mol.: 1 / Fragment: unp residues 27-396
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Strain: K12 / Gene: ECDH10B_4223, malE / Plasmid: pJF1 / Production host: Escherichia coli (E. coli) / References: UniProt: B1XC33, UniProt: P0AEX9*PLUS
#4: Protein Fused maltose transport subunit, ATP-binding component of ABC superfamily; regulatory protein


Mass: 42184.535 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Strain: K12 / Gene: ECDH10B_4224, malK / Plasmid: pKJ / Production host: Escherichia coli (E. coli) / References: UniProt: B1XC34, UniProt: P68187*PLUS

-
Maltose transporter subunit; membrane component of ABC ... , 2 types, 2 molecules FG

#2: Protein Maltose transporter subunit; membrane component of ABC superfamily


Mass: 57052.898 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Strain: K12 / Gene: ECDH10B_4222, malF / Plasmid: pFG23 / Production host: Escherichia coli (E. coli) / References: UniProt: B1XC32, UniProt: P02916*PLUS
#3: Protein Maltose transporter subunit; membrane component of ABC superfamily


Mass: 32246.227 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Strain: K12 / Gene: ECDH10B_4221, malG / Plasmid: pFG23 / Production host: Escherichia coli (E. coli) / References: UniProt: B1XC31, UniProt: P68183*PLUS

-
Sugars , 1 types, 2 molecules

#5: Polysaccharide alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose / alpha-maltose


Type: oligosaccharide, Oligosaccharide / Class: Nutrient / Mass: 342.297 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: oligosaccharide / References: alpha-maltose
DescriptorTypeProgram
DGlcpa1-4DGlcpa1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/1,2,1/[a2122h-1a_1-5]/1-1/a4-b1WURCSPDB2Glycan 1.1.0
[][a-D-Glcp]{[(4+1)][a-D-Glcp]{}}LINUCSPDB-CARE

-
Non-polymers , 4 types, 13 molecules

#6: Chemical ChemComp-PGV / (1R)-2-{[{[(2S)-2,3-DIHYDROXYPROPYL]OXY}(HYDROXY)PHOSPHORYL]OXY}-1-[(PALMITOYLOXY)METHYL]ETHYL (11E)-OCTADEC-11-ENOATE / PHOSPHATIDYLGLYCEROL / 2-VACCENOYL-1-PALMITOYL-SN-GLYCEROL-3-PHOSPHOGLYCEROL / Phosphatidylglycerol


Mass: 749.007 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C40H77O10P / Comment: phospholipid*YM
#7: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#8: Chemical ChemComp-ANP / PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER


Mass: 506.196 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H17N6O12P3 / Comment: AMP-PNP, energy-carrying molecule analogue*YM
#9: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 8 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
Sample preparation

CrystalDensity Matthews: 3.93 Å3/Da / Density % sol: 68.66 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 32% PEG 400, 0.1 M HEPES, 40 mM magnesium chloride, 50 mM sodium chloride , VAPOR DIFFUSION, SITTING DROP, temperature 293K, pH 7.5

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-D / Wavelength: 1.03326 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: May 10, 2009
RadiationMonochromator: double crystal monochromator and vertically focusing mirror
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.03326 Å / Relative weight: 1
ReflectionResolution: 2.8→20 Å / Num. all: 53826 / Num. obs: 53826 / % possible obs: 71.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Rmerge(I) obs: 0.043
Reflection shellResolution: 2.8→2.9 Å / Redundancy: 2.1 % / Mean I/σ(I) obs: 1.7 / Rsym value: 0.417 / % possible all: 23.6

-
Processing

Software
NameVersionClassification
HKL-2000data collection
PHASERphasing
REFMAC5.5.0088refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.9→19.95 Å / Cor.coef. Fo:Fc: 0.914 / Cor.coef. Fo:Fc free: 0.874 / SU B: 46.195 / SU ML: 0.38 / Cross valid method: THROUGHOUT / ESU R Free: 0.474 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.27878 2864 5.2 %RANDOM
Rwork0.23716 ---
obs0.23928 52679 77 %-
all-53826 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 92.327 Å2
Baniso -1Baniso -2Baniso -3
1--0.25 Å2-0.02 Å2-0.04 Å2
2--0.09 Å2-0.12 Å2
3---0.13 Å2
Refinement stepCycle: LAST / Resolution: 2.9→19.95 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms14536 0 153 8 14697
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0060.02215013
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg0.8941.9820411
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.21651867
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.79824.251621
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.065152494
X-RAY DIFFRACTIONr_dihedral_angle_4_deg11.5681578
X-RAY DIFFRACTIONr_chiral_restr0.0580.22348
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.02111171
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.1441.59312
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it0.267215013
X-RAY DIFFRACTIONr_scbond_it0.25835701
X-RAY DIFFRACTIONr_scangle_it0.4624.55398
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.9→2.974 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.396 74 -
Rwork0.335 1468 -
obs--29.08 %
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)
10.9517-0.10360.11174.17593.99366.9496-0.09530.02110.0571-0.18490.1509-0.4932-0.48350.1631-0.05560.5302-0.1454-0.04220.13690.11550.373831.202-5.72642.725
24.48940.33392.20766.55151.51754.47610.0054-0.32190.1540.7519-0.1119-0.26790.4215-0.24690.10650.61390.122-0.12090.2520.04890.093830.03-34.46552.453
36.2126-6.40651.269912.9645-1.15646.00540.21230.22091.2245-0.0839-0.3574-3.5056-0.71271.87410.14510.4815-0.2546-0.22251.17810.05352.036259.7-13.66250.621
41.83410.4255-0.1852.8476-1.01214.4940.0843-0.22910.0065-0.2157-0.16110.65830.8015-0.87670.07680.1744-0.176-0.00110.3392-0.09640.3193-12.537-72.924-13.214
515.40758.063811.124413.14457.789813.5239-2.05211.70052.2146-3.54160.95142.7374-2.7569-0.17471.10072.47630.2545-0.8170.83420.31151.44282.95-19.315-9.246
60.55660.28160.91351.86611.10784.7933-0.0026-0.26220.2601-0.2067-0.38740.488-0.3155-0.91050.390.06850.11830.03920.3561-0.04590.4033-5.734-49.431-3.818
71.64281.79270.97533.98021.78153.7533-0.06290.0180.0737-0.17360.0980.0848-0.33670.1615-0.03510.11960.02270.11880.2905-0.0490.188612.383-45.9547.253
80.59771.5434-0.57239.50713.00144.77790.1653-0.03180.04030.03050.0316-0.2578-0.18060.4352-0.19690.13330.03680.08020.3551-0.01280.22289.68-54.4720.483
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A2 - 371
2X-RAY DIFFRACTION1A2501
3X-RAY DIFFRACTION1A1501
4X-RAY DIFFRACTION2B2 - 228
5X-RAY DIFFRACTION2B2502
6X-RAY DIFFRACTION2B1502
7X-RAY DIFFRACTION3B229 - 371
8X-RAY DIFFRACTION4E1 - 370
9X-RAY DIFFRACTION4E2002
10X-RAY DIFFRACTION5F18 - 64
11X-RAY DIFFRACTION6F65 - 503
12X-RAY DIFFRACTION6F4001
13X-RAY DIFFRACTION6F2001
14X-RAY DIFFRACTION7G2 - 216
15X-RAY DIFFRACTION8G217 - 283

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more