[English] 日本語
Yorodumi
- PDB-3hn0: CRYSTAL STRUCTURE OF AN ABC TRANSPORTER (BDI_1369) FROM PARABACTE... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 3hn0
TitleCRYSTAL STRUCTURE OF AN ABC TRANSPORTER (BDI_1369) FROM PARABACTEROIDES DISTASONIS AT 1.75 A RESOLUTION
ComponentsNitrate transport protein
KeywordsTRANSPORT PROTEIN / ABC TRANSPORTER / STRUCTURAL GENOMICS / JOINT CENTER FOR STRUCTURAL GENOMICS / JCSG / PROTEIN STRUCTURE INITIATIVE / PSI-2
Function / homologyABC-type uncharacterised transport system, substrate-binding component, TM0202 type / Periplasmic binding protein-like II / D-Maltodextrin-Binding Protein; domain 2 / 3-Layer(aba) Sandwich / Alpha Beta / DI(HYDROXYETHYL)ETHER / PHOSPHATE ION / ABC transporter substrate-binding protein
Function and homology information
Biological speciesParabacteroides distasonis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.75 Å
AuthorsJoint Center for Structural Genomics (JCSG)
CitationJournal: To be published
Title: Crystal structure of Nitrate transport protein (YP_001302749.1) from Parabacteroides distasonis ATCC 8503 at 1.75 A resolution
Authors: Joint Center for Structural Genomics (JCSG)
History
DepositionMay 29, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 7, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2Nov 1, 2017Group: Refinement description / Category: software / Item: _software.classification / _software.name
Revision 1.3Jul 24, 2019Group: Data collection / Derived calculations / Refinement description
Category: software / struct_conn
Item: _software.classification / _software.contact_author ..._software.classification / _software.contact_author / _software.contact_author_email / _software.language / _software.location / _software.name / _software.type / _software.version / _struct_conn.pdbx_leaving_atom_flag
Revision 1.4Feb 1, 2023Group: Database references / Derived calculations / Category: database_2 / 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
Revision 1.5Oct 30, 2024Group: Data collection / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_entry_details / pdbx_modification_feature
Item: _pdbx_entry_details.has_protein_modification

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Nitrate transport protein
B: Nitrate transport protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)63,4919
Polymers62,9802
Non-polymers5117
Water10,701594
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: Nitrate transport protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,8155
Polymers31,4901
Non-polymers3254
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
B: Nitrate transport protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,6764
Polymers31,4901
Non-polymers1863
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)47.627, 97.755, 114.015
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
DetailsTHIS ENTRY CONTAINS THE CRYSTALLOGRAPHIC ASYMMETRIC UNIT WHICH CONSISTS OF 2 CHAINS.

-
Components

#1: Protein Nitrate transport protein


Mass: 31489.857 Da / Num. of mol.: 2 / Fragment: sequence database residues 21-302
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Parabacteroides distasonis (bacteria) / Gene: BDI_1369, YP_001302749.1 / Plasmid: SpeedET / Production host: Escherichia coli (E. coli) / Strain (production host): HK100 / References: UniProt: A6LBR3
#2: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: PO4
#3: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O3
#4: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C2H6O2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 594 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY
Sequence detailsTHIS CONSTRUCT (RESIDUES 21-302) WAS EXPRESSED WITH A PURIFICATION TAG MGSDKIHHHHHHENLYFQG. THE TAG ...THIS CONSTRUCT (RESIDUES 21-302) WAS EXPRESSED WITH A PURIFICATION TAG MGSDKIHHHHHHENLYFQG. THE TAG WAS REMOVED WITH TEV PROTEASE LEAVING ONLY A GLYCINE (0) FOLLOWED BY THE TARGET SEQUENCE.

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.11 Å3/Da / Density % sol: 41.63 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 4.6
Details: 0.2000M NH4H2PO4, 20.0000% PEG-3350, No Buffer pH 4.6, VAPOR DIFFUSION, SITTING DROP, NANODROP, temperature 277K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL11-1 / Wavelength: 0.91162,0.97889
DetectorType: MARMOSAIC 325 mm CCD / Detector: CCD / Date: Feb 22, 2009 / Details: Flat mirror (vertical focusing)
RadiationMonochromator: Single crystal Si(111) bent monochromator (horizontal focusing)
Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.911621
20.978891
ReflectionResolution: 1.75→29.709 Å / Num. obs: 54325 / % possible obs: 99.6 % / Redundancy: 3.7 % / Biso Wilson estimate: 19.443 Å2 / Rmerge(I) obs: 0.077 / Rsym value: 0.077 / Net I/σ(I): 6.144
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allRsym value% possible all
1.75-1.83.70.4351.81454639000.43599
1.8-1.843.70.3672.11430938570.36799
1.84-1.93.70.3012.51397737690.30199.7
1.9-1.963.70.243.21347036220.2499.5
1.96-2.023.70.184.21312135360.1899.5
2.02-2.093.70.1544.81281334530.15499.5
2.09-2.173.70.135.71223033080.1399.7
2.17-2.263.70.1136.51184931980.113100
2.26-2.363.70.0997.21145530860.09999.8
2.36-2.473.70.0917.81091229470.09199.8
2.47-2.613.70.08681038928100.08699.9
2.61-2.773.70.0827.9984626670.08299.9
2.77-2.963.70.0778.2926625290.077100
2.96-3.23.60.0688.3857323520.068100
3.2-3.53.60.0599.7791321700.059100
3.5-3.913.70.05211725619870.052100
3.91-4.523.60.0511.6633317480.05100
4.52-5.533.60.0511.2539115100.0599.8
5.53-7.833.50.05510.5417411960.05599.6
7.83-29.713.30.0511.122126800.0596.9

-
Phasing

PhasingMethod: MAD

-
Processing

Software
NameVersionClassificationNB
REFMAC5.5.0053refinement
PHENIXrefinement
SHELXphasing
MolProbity3beta29model building
SCALA3.2.5data scaling
PDB_EXTRACT3.006data extraction
MOSFLMdata reduction
SHELXDphasing
autoSHARPphasing
RefinementMethod to determine structure: MAD / Resolution: 1.75→29.709 Å / Cor.coef. Fo:Fc: 0.963 / Cor.coef. Fo:Fc free: 0.945 / Occupancy max: 1 / Occupancy min: 0.25 / SU B: 5.496 / SU ML: 0.08 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.123 / ESU R Free: 0.118
Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES
Details: 1. HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. 2. ATOM RECORD CONTAINS RESIDUAL B FACTORS ONLY. 3. A MET-INHIBITION PROTOCOL WAS USED FOR SELENOMETHIONINE INCORPORATION DURING PROTEIN ...Details: 1. HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. 2. ATOM RECORD CONTAINS RESIDUAL B FACTORS ONLY. 3. 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 TO ACCOUNT FOR THE REDUCED SCATTERING POWER DUE TO PARTIAL S-MET INCORPORATION. 4. PHOSPHATE (PO4), ETHYLENE GLYCOL (EDO), AND POLYETHYLENE GLYCOL (PEG) FROM THE CRYSTALLIZATION/CRYOPROTECTANT SOLUTIONS HAVE BEEN MODELED INTO THE SOLVENT STRUCTURE.
RfactorNum. reflection% reflectionSelection details
Rfree0.21 2759 5.1 %RANDOM
Rwork0.17 ---
obs0.172 54272 99.54 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso max: 74.21 Å2 / Biso mean: 22.703 Å2 / Biso min: 3.05 Å2
Baniso -1Baniso -2Baniso -3
1-0.19 Å20 Å20 Å2
2--0.34 Å20 Å2
3----0.54 Å2
Refinement stepCycle: LAST / Resolution: 1.75→29.709 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4325 0 31 594 4950
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0170.0224667
X-RAY DIFFRACTIONr_bond_other_d0.0010.023153
X-RAY DIFFRACTIONr_angle_refined_deg1.5061.9886404
X-RAY DIFFRACTIONr_angle_other_deg0.92937781
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.6675631
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.89724.286189
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.38215792
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.0191526
X-RAY DIFFRACTIONr_chiral_restr0.0870.2751
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.0215235
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02907
X-RAY DIFFRACTIONr_mcbond_it2.00132930
X-RAY DIFFRACTIONr_mcbond_other0.57531166
X-RAY DIFFRACTIONr_mcangle_it3.25154786
X-RAY DIFFRACTIONr_scbond_it4.85381737
X-RAY DIFFRACTIONr_scangle_it7.134111589
LS refinement shellResolution: 1.75→1.795 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.258 199 -
Rwork0.215 3698 -
all-3897 -
obs--98.86 %
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)
10.61780.0180.13461.1349-0.05840.6420.0141-0.06180.00940.0356-0.00780.03260.04040.0198-0.00640.00390.00050.00080.0083-0.00060.00369.564514.007328.3075
21.2505-0.5048-0.32141.4475-0.13241.5018-0.1076-0.1054-0.24570.11340.02010.08570.1222-0.03010.08750.04920.01210.02810.020.02270.0502-1.372-1.11461.5297
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A23 - 302
2X-RAY DIFFRACTION2B23 - 302

+
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