[English] 日本語
Yorodumi
- PDB-2qlw: Crystal structure of rhamnose mutarotase RhaU of Rhizobium legumi... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 2qlw
TitleCrystal structure of rhamnose mutarotase RhaU of Rhizobium leguminosarum
ComponentsRhaU
KeywordsISOMERASE / RhaU / mutarotase / Rhizobium leguminosarum
Function / homology
Function and homology information


L-rhamnose mutarotase / L-rhamnose mutarotase activity / rhamnose catabolic process / cytoplasm
Similarity search - Function
L-rhamnose mutarotase / Rhamnose/fucose mutarotase / L-rhamnose mutarotase / Alpha-Beta Plaits - #100 / Dimeric alpha-beta barrel / Alpha-Beta Plaits / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
FORMIC ACID / L-rhamnose mutarotase
Similarity search - Component
Biological speciesRhizobium leguminosarum bv. trifolii (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.6 Å
AuthorsCarpena, X. / Loewen, P.C.
CitationJournal: J.Bacteriol. / Year: 2008
Title: RhaU of Rhizobium leguminosarum is a rhamnose mutarotase.
Authors: Richardson, J.S. / Carpena, X. / Switala, J. / Perez-Luque, R. / Donald, L.J. / Loewen, P.C. / Oresnik, I.J.
History
DepositionJul 13, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 4, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Derived calculations / Version format compliance
Revision 1.2Oct 18, 2017Group: Refinement description / Category: software
Revision 1.3Nov 20, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / pdbx_struct_conn_angle / pdbx_struct_special_symmetry / struct_conn / struct_conn_type / struct_ncs_dom_lim / 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_asym_id / _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.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_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.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_asym_id / _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_asym_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_conn.ptnr2_label_seq_id / _struct_conn_type.id / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_seq_id / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: RhaU
B: RhaU
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,77920
Polymers33,9942
Non-polymers78518
Water3,963220
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5840 Å2
ΔGint-35 kcal/mol
Surface area10920 Å2
MethodPISA
2
A: RhaU
B: RhaU
hetero molecules

A: RhaU
B: RhaU
hetero molecules


Theoretical massNumber of molelcules
Total (without water)69,55740
Polymers67,9874
Non-polymers1,57036
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation6_555x,x-y,-z1
Buried area13850 Å2
ΔGint-93 kcal/mol
Surface area19670 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)69.241, 69.241, 101.106
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number153
Space group name H-MP3212
Components on special symmetry positions
IDModelComponents
11B-1080-

HOH

Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B

NCS domain segments:

Component-ID: 1 / Ens-ID: 1 / Beg auth comp-ID: MSE / Beg label comp-ID: MSE / End auth comp-ID: PHE / End label comp-ID: PHE / Refine code: 6 / Auth seq-ID: 1 - 103 / Label seq-ID: 39 - 141

Dom-IDAuth asym-IDLabel asym-ID
1AA
2BB

-
Components

#1: Protein RhaU


Mass: 16996.836 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rhizobium leguminosarum bv. trifolii (bacteria)
Gene: rhaU / Production host: Escherichia coli (E. coli) / References: UniProt: Q7BSH1
#2: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#3: Chemical
ChemComp-FMT / FORMIC ACID


Mass: 46.025 Da / Num. of mol.: 16 / Source method: obtained synthetically / Formula: CH2O2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 220 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.72 Å3/Da / Density % sol: 54.76 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 4.6
Details: 2M Sodium Formate, 0.1M Sodium Acetate pH 4.6, 20% Glycerol , VAPOR DIFFUSION, HANGING DROP, temperature 298K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: BM16 / Wavelength: 0.9079 Å
DetectorType: MAR CCD 165 mm / Detector: CCD / Date: Feb 23, 2006 / Details: Mirrors
RadiationMonochromator: SI 111 / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9079 Å / Relative weight: 1
ReflectionRedundancy: 5.7 % / Av σ(I) over netI: 11.2 / Number: 203502 / Rmerge(I) obs: 0.097 / Χ2: 0.95 / D res high: 1.6 Å / D res low: 30 Å / Num. obs: 35978 / % possible obs: 97.1
Diffraction reflection shell
Highest resolution (Å)Lowest resolution (Å)% possible obs (%)IDRmerge(I) obsChi squaredRedundancy
3.453088.810.0621.085.1
2.743.4598.710.0640.9535.7
2.392.7498.810.0790.9645.7
2.172.3998.610.090.9675.7
2.022.1798.410.110.9345.7
1.92.029810.1490.915.7
1.81.997.810.2380.9055.7
1.721.897.610.330.9095.8
1.661.7297.310.4490.9575.7
1.61.669710.5890.985.6
ReflectionResolution: 1.6→30 Å / Num. all: 35978 / Num. obs: 35978 / % possible obs: 97.1 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 5.7 % / Rmerge(I) obs: 0.097 / Χ2: 0.954 / Net I/σ(I): 11.2
Reflection shellResolution: 1.6→1.66 Å / Redundancy: 5.6 % / Rmerge(I) obs: 0.589 / Mean I/σ(I) obs: 3.2 / Num. unique all: 3574 / Χ2: 0.98 / % possible all: 97

-
Phasing

PhasingMethod: SAD

-
Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
SHELXphasing
REFMACrefinement
PDB_EXTRACT2data extraction
DNAdata collection
SHELXDphasing
RefinementMethod to determine structure: SAD / Resolution: 1.6→19.99 Å / Cor.coef. Fo:Fc: 0.966 / Cor.coef. Fo:Fc free: 0.954 / SU B: 2.496 / SU ML: 0.044 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.072 / ESU R Free: 0.074 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.18 1786 5 %RANDOM
Rwork0.152 ---
all0.153 35783 --
obs0.153 35783 97.15 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 10.823 Å2
Baniso -1Baniso -2Baniso -3
1-0.08 Å20.04 Å20 Å2
2--0.08 Å20 Å2
3----0.11 Å2
Refinement stepCycle: LAST / Resolution: 1.6→19.99 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1748 0 50 220 2018
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0180.0211946
X-RAY DIFFRACTIONr_bond_other_d0.0070.021322
X-RAY DIFFRACTIONr_angle_refined_deg1.691.9542620
X-RAY DIFFRACTIONr_angle_other_deg1.71133261
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.3965226
X-RAY DIFFRACTIONr_dihedral_angle_2_deg30.34624.30193
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.07415361
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.659159
X-RAY DIFFRACTIONr_chiral_restr0.1360.2280
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.022056
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02359
X-RAY DIFFRACTIONr_nbd_refined0.2270.2385
X-RAY DIFFRACTIONr_nbd_other0.2140.21375
X-RAY DIFFRACTIONr_nbtor_refined0.1790.2910
X-RAY DIFFRACTIONr_nbtor_other0.0890.2902
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1610.2149
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1970.210
X-RAY DIFFRACTIONr_symmetry_vdw_other0.20.243
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1290.215
X-RAY DIFFRACTIONr_mcbond_it1.5191.51419
X-RAY DIFFRACTIONr_mcbond_other0.3111.5444
X-RAY DIFFRACTIONr_mcangle_it1.78221849
X-RAY DIFFRACTIONr_scbond_it3.273891
X-RAY DIFFRACTIONr_scangle_it4.5354.5765
Refine LS restraints NCS

Dom-ID: 1 / Auth asym-ID: A / Ens-ID: 1 / Number: 1381 / Refine-ID: X-RAY DIFFRACTION

TypeRms dev position (Å)Weight position
LOOSE POSITIONAL0.465
LOOSE THERMAL1.2610
LS refinement shellResolution: 1.6→1.641 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.272 118 -
Rwork0.213 2483 -
obs-2601 96.87 %
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)
10.614-0.0467-0.30860.75120.36070.6761-0.01250.0065-0.07960.0735-0.09040.10760.071-0.09250.1029-0.0185-0.01450.0102-0.0268-0.0235-0.01633.417816.854410.8443
20.606-0.1951-0.01271.0469-0.36940.688-0.00260.10240.0363-0.0275-0.06-0.0715-0.0390.01630.0626-0.02690.0058-0.0111-0.01960.0084-0.031114.588627.0149-5.2807
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA0 - 1062 - 108
2X-RAY DIFFRACTION2BB0 - 1062 - 108

+
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