[English] 日本語
Yorodumi
- PDB-3qxb: Crystal structure of a Putative Xylose isomerase (YP_426450.1) fr... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 3qxb
TitleCrystal structure of a Putative Xylose isomerase (YP_426450.1) from RHODOSPIRILLUM RUBRUM ATCC 11170 at 1.90 A resolution
ComponentsPutative Xylose isomerase
KeywordsISOMERASE / Structural Genomics / Joint Center for Structural Genomics / JCSG / Protein Structure Initiative / PSI-biology
Function / homology
Function and homology information


isomerase activity / metal ion binding
Similarity search - Function
Divalent-metal-dependent TIM barrel enzymes / Xylose isomerase-like, TIM barrel domain / Xylose isomerase-like TIM barrel / Xylose isomerase-like superfamily / TIM Barrel / Alpha-Beta Barrel / Alpha Beta
Similarity search - Domain/homology
ACETATE ION / : / : / Xylose isomerase-like TIM barrel
Similarity search - Component
Biological speciesRhodospirillum rubrum (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.9 Å
AuthorsJoint Center for Structural Genomics (JCSG)
CitationJournal: To be published
Title: Crystal structure of a Putative Xylose isomerase (YP_426450.1) from RHODOSPIRILLUM RUBRUM ATCC 11170 at 1.90 A resolution
Authors: Joint Center for Structural Genomics (JCSG)
History
DepositionMar 1, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 23, 2011Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 8, 2017Group: Refinement description / Category: software / Item: _software.classification / _software.name
Revision 1.3Feb 1, 2023Group: Database references / Derived calculations
Category: database_2 / pdbx_struct_conn_angle ...database_2 / pdbx_struct_conn_angle / struct_conn / 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_atom_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_auth_comp_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_alt_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr2_label_atom_id / _pdbx_struct_conn_angle.ptnr2_label_comp_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_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.pdbx_ptnr1_label_alt_id / _struct_conn.pdbx_ptnr2_label_alt_id / _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_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: Putative Xylose isomerase
B: Putative Xylose isomerase
C: Putative Xylose isomerase
D: Putative Xylose isomerase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)147,93342
Polymers145,8264
Non-polymers2,10738
Water17,511972
1
A: Putative Xylose isomerase
B: Putative Xylose isomerase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)74,07723
Polymers72,9132
Non-polymers1,16421
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8010 Å2
ΔGint-118 kcal/mol
Surface area20160 Å2
MethodPISA
2
C: Putative Xylose isomerase
D: Putative Xylose isomerase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)73,85619
Polymers72,9132
Non-polymers94217
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7050 Å2
ΔGint-117 kcal/mol
Surface area20350 Å2
MethodPISA
Unit cell
Length a, b, c (Å)76.188, 94.903, 173.197
Angle α, β, γ (deg.)90.000, 93.040, 90.000
Int Tables number5
Space group name H-MC121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
31C
41D

NCS domain segments:
Dom-IDComponent-IDEns-IDRefine codeAuth asym-IDAuth seq-ID
1116A0 - 295
2116B0 - 295
3116C0 - 295
4116D0 - 295
DetailsCRYSTAL PACKING ANALYSIS SUGGESTS THE ASSIGNMENT OF A DIMER AS THE SIGNIFICANT OLIGOMERIZATION STATE.

-
Components

-
Protein , 1 types, 4 molecules ABCD

#1: Protein
Putative Xylose isomerase / / Xylose isomerase-like TIM barrel


Mass: 36456.527 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rhodospirillum rubrum (bacteria) / Strain: ATCC 11170 / Gene: Rru_A1362 / Plasmid: SpeedET / Production host: Escherichia Coli (E. coli) / Strain (production host): HK100 / References: UniProt: Q2RUN2

-
Non-polymers , 6 types, 1010 molecules

#2: Chemical
ChemComp-FE / FE (III) ION / Iron


Mass: 55.845 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: Fe
#3: Chemical
ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: Mn
#4: Chemical
ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: Cl
#5: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 13 / Source method: obtained synthetically / Formula: C2H6O2
#6: Chemical
ChemComp-ACT / ACETATE ION / Acetate


Mass: 59.044 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C2H3O2
#7: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 972 / Source method: isolated from a natural source / Formula: H2O

-
Details

Sequence detailsTHIS CONSTRUCT WAS EXPRESSED WITH A PURIFICATION TAG MGSDKIHHHHHHENLYFQG.

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.14 Å3/Da / Density % sol: 42.63 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 7.1
Details: 0.2M NH4Acetate, 20.0% PEG-3350, No Buffer pH 7.1, NANODROP, VAPOR DIFFUSION, SITTING DROP, temperature 277K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL9-2 / Wavelength: 0.97911
DetectorType: MARMOSAIC 325 mm CCD / Detector: CCD / Date: Jul 30, 2009 / Details: double crystal monochromator
RadiationMonochromator: double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97911 Å / Relative weight: 1
ReflectionResolution: 1.9→29.683 Å / Num. obs: 96564 / % possible obs: 99.8 % / Redundancy: 2.9 % / Biso Wilson estimate: 20.08 Å2 / Rmerge(I) obs: 0.102 / Rsym value: 0.102 / Net I/σ(I): 8
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allRsym value% possible all
1.9-1.952.80.4322.22012471070.432100
1.95-22.80.3652.11960269170.365100
2-2.062.80.3182.41936468030.318100
2.06-2.122.80.25431868665580.254100
2.12-2.192.90.2193.41821063830.219100
2.19-2.272.90.18541767761840.185100
2.27-2.362.90.1624.61698159340.162100
2.36-2.452.90.154.71645057460.15100
2.45-2.562.90.1395.11572254900.139100
2.56-2.692.90.1345.11504752520.134100
2.69-2.832.90.12551430349990.12599.9
2.83-32.90.1046.21360847250.10499.9
3-3.212.90.0916.81287944670.09199.8
3.21-3.472.90.0777.81181741160.07799.6
3.47-3.82.90.06691112338310.06699.6
3.8-4.252.90.0599.9985134120.05999.4
4.25-4.912.90.05910.2873630200.05999.2
4.91-6.012.90.0669.5736425640.06698.8
6.01-8.52.80.0679565519860.06798.4
8.5-29.6832.80.0638.9297610700.06395.8

-
Phasing

PhasingMethod: SAD

-
Processing

Software
NameVersionClassificationNB
MolProbity3beta29model building
PDB_EXTRACT3.1data extraction
SHELXphasing
SHARPphasing
SCALA3.2.5data scaling
REFMAC5.5.0110refinement
MOSFLMdata reduction
autoSHARPphasing
RefinementMethod to determine structure: SAD / Resolution: 1.9→29.683 Å / Cor.coef. Fo:Fc: 0.969 / Cor.coef. Fo:Fc free: 0.949 / Occupancy max: 1 / Occupancy min: 0.15 / SU B: 6.081 / SU ML: 0.09 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.126
Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES
Details: 1. HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. 2. ATOM RECORD CONTAINS SUM OF TLS AND RESIDUAL B FACTORS. 3. ANISOU RECORD CONTAINS SUM OF TLS AND RESIDUAL U FACTORS. 4. WATERS WERE ...Details: 1. HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. 2. ATOM RECORD CONTAINS SUM OF TLS AND RESIDUAL B FACTORS. 3. ANISOU RECORD CONTAINS SUM OF TLS AND RESIDUAL U FACTORS. 4. WATERS WERE EXCLUDED FROM AUTOMATIC TLS ASSIGNMENT. 5. 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. 6. THE IDENTITY OF THE METAL SITES WAS TENTATIVELY ASSIGNED AS A PARTIAL OCCUPANCY IRON AND MANGANESE. X-RAY FLUORESCENCE EMISSION SPECTRA SHOWED PEAKS CORRESPONDING TO ZN, FE AND MN. ANOMALOUS DIFFERENCE FOURIER (ADF) MAPS FROM DATA COLLECTED ABOVE AND BELOW THE K-ABSORPTION EDGE OF ZINC, IRON AND MANGANESE SUGGESTED THAT THE SITES CONTAINED A MIXTURE OF METALS WITH IRON AND MANGANESE BEING MORE PREVALENT THAN ZINC. BASED ON THE LARGER DROP IN ADF PEAK HEIGHT ACROSS THE FE K-EDGE FOR THE 301/302 SITE, IT WAS MODELED WITH MORE IRON THAN MANGANESE. THE SMALLER CHANGE IN PEAK HEIGHT FOR THE 303/304 SITE SUGGESTED MN WAS MORE PREVALENT AT THIS SITE. IN ADDITION, THE LOWER ELECTRON DENSITY AND ANOMALOUS PEAK HEIGHT AT THE 303/304 SITE SUGGESTED THAT THE SITE MIGHT NOT BE FULLY OCCUPIED. 7. ACETATE ION (ACT) AND 1,2-ETHANEDIOL (EDO) MOLECULES FROM THE CRYSTALLIZATION/CRYOPROTECTION SOLUTION ARE MODELED.
RfactorNum. reflection% reflectionSelection details
Rfree0.1916 4830 5 %RANDOM
Rwork0.1498 ---
obs0.1519 96562 99.72 %-
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: 59.76 Å2 / Biso mean: 27.6657 Å2 / Biso min: 10.3 Å2
Baniso -1Baniso -2Baniso -3
1-0.18 Å20 Å2-1.6 Å2
2---0.92 Å20 Å2
3---0.58 Å2
Refinement stepCycle: LAST / Resolution: 1.9→29.683 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9445 0 89 972 10506
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0170.0229927
X-RAY DIFFRACTIONr_bond_other_d0.0010.026706
X-RAY DIFFRACTIONr_angle_refined_deg1.4681.95513513
X-RAY DIFFRACTIONr_angle_other_deg0.932316198
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.24451213
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.51823.235473
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.892151533
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.4171576
X-RAY DIFFRACTIONr_chiral_restr0.0880.21433
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.02111191
X-RAY DIFFRACTIONr_gen_planes_other0.0010.022157
X-RAY DIFFRACTIONr_mcbond_it0.6961.56037
X-RAY DIFFRACTIONr_mcbond_other0.2291.52390
X-RAY DIFFRACTIONr_mcangle_it1.16629675
X-RAY DIFFRACTIONr_scbond_it2.31233890
X-RAY DIFFRACTIONr_scangle_it3.3884.53838
Refine LS restraints NCS

Ens-ID: 1 / Number: 3775 / Refine-ID: X-RAY DIFFRACTION

Dom-IDAuth asym-IDTypeRms dev position (Å)Weight position
1ALOOSE POSITIONAL0.315
2BLOOSE POSITIONAL0.225
3CLOOSE POSITIONAL0.245
4DLOOSE POSITIONAL0.245
1ALOOSE THERMAL1.8810
2BLOOSE THERMAL1.5810
3CLOOSE THERMAL1.5110
4DLOOSE THERMAL1.8910
LS refinement shellResolution: 1.9→1.949 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.262 326 -
Rwork0.23 6755 -
all-7081 -
obs--99.99 %
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)
11.09540.47940.23150.65010.35510.4056-0.17780.24860.1374-0.12840.1420.046-0.05970.1290.03580.0923-0.06860.00690.10140.04680.0478-3.07822.22860.429
21.05510.15430.24820.9673-0.03310.4112-0.08030.02410.1516-0.05020.05730.18320.0269-0.05790.02290.0482-0.03180.00510.03920.02480.0864-28.27516.65872.097
31.0625-0.040.31330.8110.02130.61590.01770.0913-0.05890.00990.002-0.06870.03630.122-0.01970.03740.02840.01770.0564-0.01580.0343-17.9839.8216.404
41.5451-0.26040.36770.6086-0.2050.7106-0.0432-0.2659-0.06130.04730.05230.06010.0003-0.151-0.0090.03770.02040.02790.08040.00190.0294-44.15314.8226.121
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A0 - 296
2X-RAY DIFFRACTION1A301 - 304
3X-RAY DIFFRACTION2B0 - 295
4X-RAY DIFFRACTION2B301 - 304
5X-RAY DIFFRACTION3C0 - 295
6X-RAY DIFFRACTION3C301 - 304
7X-RAY DIFFRACTION4D0 - 295
8X-RAY DIFFRACTION4D301 - 304

+
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