[English] 日本語
Yorodumi
- PDB-2p4g: CRYSTAL STRUCTURE OF A PYRIMIDINE REDUCTASE-LIKE PROTEIN (DIP1392... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 2p4g
TitleCRYSTAL STRUCTURE OF A PYRIMIDINE REDUCTASE-LIKE PROTEIN (DIP1392) FROM CORYNEBACTERIUM DIPHTHERIAE NCTC AT 2.30 A RESOLUTION
ComponentsHypothetical protein
KeywordsOXIDOREDUCTASE / PYRIMIDINE REDUCTASE-LIKE PROTEIN / STRUCTURAL GENOMICS / JOINT CENTER FOR STRUCTURAL GENOMICS / JCSG / PROTEIN STRUCTURE INITIATIVE / PSI-2
Function / homology
Function and homology information


5-amino-6-(5-phosphoribosylamino)uracil reductase activity / riboflavin biosynthetic process
Similarity search - Function
Bacterial bifunctional deaminase-reductase, C-terminal / RibD C-terminal domain / Dihydrofolate Reductase, subunit A / Dihydrofolate Reductase, subunit A / Dihydrofolate reductase-like domain superfamily / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
NITRATE ION / RibD_C domain-containing protein
Similarity search - Component
Biological speciesCorynebacterium diphtheriae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.3 Å
AuthorsJoint Center for Structural Genomics (JCSG)
CitationJournal: To be published
Title: Crystal structure of hypothetical protein (NP_939744.1) from Corynebacterium diphtheriae at 2.30 A resolution
Authors: Joint Center for Structural Genomics (JCSG)
History
DepositionMar 12, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 27, 2007Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Advisory / Derived calculations ...Advisory / Derived calculations / Source and taxonomy / Version format compliance
Revision 1.3Oct 18, 2017Group: Refinement description / Category: software / Item: _software.classification / _software.name
Revision 1.4Oct 25, 2017Group: Author supporting evidence / Category: pdbx_struct_assembly_auth_evidence
Revision 1.5Jan 25, 2023Group: Database references / Derived calculations
Category: database_2 / struct_conn ...database_2 / 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 / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Remark 300 BIOMOLECULE: 1 THIS ENTRY CONTAINS THE CRYSTALLOGRAPHIC ASYMMETRIC UNIT WHICH CONSISTS OF 1 ... BIOMOLECULE: 1 THIS ENTRY CONTAINS THE CRYSTALLOGRAPHIC ASYMMETRIC UNIT WHICH CONSISTS OF 1 CHAIN(S). SEE REMARK 350 FOR INFORMATION ON GENERATING THE BIOLOGICAL MOLECULE(S). SIZE EXCLUSION CHROMATOGRAPHY SUPPORTS THE ASSIGNMENT OF A DIMER AS A BIOLOGICALLY SIGNIFICANT OLIGOMERIZATION STATE.
Remark 999 SEQUENCE THE CONSTRUCT WAS EXPRESSED WITH A PURIFICATION TAG MGSDKIHHHHHHENLYFQG. THE TAG WAS ... SEQUENCE THE CONSTRUCT WAS EXPRESSED WITH A PURIFICATION TAG MGSDKIHHHHHHENLYFQG. THE TAG WAS REMOVED WITH TEV PROTEASE LEAVING ONLY A GLYCINE (0), FOLLOWED BY THE TARGET SEQUENCE.

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Hypothetical protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,47817
Polymers29,4851
Non-polymers99316
Water2,036113
1
A: Hypothetical protein
hetero molecules

A: Hypothetical protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)60,95634
Polymers58,9702
Non-polymers1,98632
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_665-x+1,-y+1,z1
Buried area8720 Å2
ΔGint50 kcal/mol
Surface area21300 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)113.510, 113.510, 55.940
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number172
Space group name H-MP64
DetailsSIZE EXCLUSION CHROMATOGRAPHY SUPPORTS THE ASSIGNMENT OF A DIMER AS A BIOLOGICALLY SIGNIFICANT OLIGOMERIZATION STATE.

-
Components

#1: Protein Hypothetical protein /


Mass: 29485.064 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Corynebacterium diphtheriae (bacteria) / Strain: NCTC 13129 / Gene: NP_939744.1, DIP1392 / Plasmid: speedET / Production host: Escherichia coli (E. coli) / Strain (production host): HK100 / References: UniProt: Q6NGV8
#2: Chemical ChemComp-NO3 / NITRATE ION / Nitrate


Mass: 62.005 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: NO3
#3: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 15 / Source method: obtained synthetically / Formula: C2H6O2
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 113 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 2

-
Sample preparation

Crystal
IDDensity Matthews (Å3/Da)Density % sol (%)Description
13.5365.12TWO CRYSTALS WERE USED FOR THE SOLUTION OF THIS STRUCTURE. 2.47 ANGSTROM MAD DA TA COLLECTED FROM ONE CRYSTAL WAS USED TO PHASE THE STRUCTURE. THE RESOLUTION OF THE INITIAL MODEL WAS THEN EXTENDED USING THE AMPLITUDES FROM A SECOND CRYSTAL THAT DIFFRACTED TO 2.30 ANGSTROMS. THE CRYSTALS ARE TWINNED. THE STRUCTURE WAS P HASED WITHOUT DETWINNING THE DATA. THE DATA REDUCTIONS STATISTICS ARE PRIOR TO D ETWINNING. A TOTAL OF 130 REFLECTIONS COULD NOT BE DETWINNED BECAUSE THEIR TWIN- RELATED REFLECTIONS WERE NOT RECORDED.
2TWO CRYSTALS WERE USED FOR THE SOLUTION OF THIS STRUCTURE. 2.47 ANGSTROM MAD DA TA COLLECTED FROM ONE CRYSTAL WAS USED TO PHASE THE STRUCTURE. THE RESOLUTION OF THE INITIAL MODEL WAS THEN EXTENDED USING THE AMPLITUDES FROM A SECOND CRYSTAL THAT DIFFRACTED TO 2.30 ANGSTROMS. THE CRYSTALS ARE TWINNED. THE STRUCTURE WAS P HASED WITHOUT DETWINNING THE DATA. THE DATA REDUCTIONS STATISTICS ARE PRIOR TO D ETWINNING. A TOTAL OF 130 REFLECTIONS COULD NOT BE DETWINNED BECAUSE THEIR TWIN- RELATED REFLECTIONS WERE NOT RECORDED.
Crystal grow
Temperature (K)Crystal-IDMethodDetailspH
2771vapor diffusion, sitting dropNANODROP, 0.2M Potassium nitrate, 20.0% PEG 3350, VAPOR DIFFUSION, SITTING DROP, temperature 277K
2772vapor diffusion, sitting dropNANODROP, 0.2M Potassium nitrate, 20.0% PEG 3350, No Buffer pH 6.9, VAPOR DIFFUSION, SITTING DROP, temperature 277K6.9

-
Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
21002
Diffraction source
SourceSiteBeamlineIDWavelength (Å)
SYNCHROTRONALS 5.0.311
SYNCHROTRONSSRL BL9-220.97922, 0.97939, 0.91162
Detector
TypeIDDetectorDateDetails
ADSC QUANTUM 3151CCDSep 22, 2006
MARMOSAIC 325 mm CCD2CCDJun 18, 2006Flat collimating mirror, toroid focusing mirror
Radiation
IDMonochromatorProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1Single, cylindrically bent, asymmetrically cut Si(220) crystalSINGLE WAVELENGTHMx-ray1
2Double crystalMADMx-ray1
Radiation wavelength
IDWavelength (Å)Relative weight
111
20.979221
30.979391
40.911621
ReflectionResolution: 2.3→28.273 Å / Num. obs: 18260 / % possible obs: 97.3 % / Redundancy: 3.66 % / Biso Wilson estimate: 46.09 Å2 / Rmerge(I) obs: 0.052 / Net I/σ(I): 11.61
Reflection shell
Resolution (Å)Rmerge(I) obsMean I/σ(I) obsNum. measured obsDiffraction-ID% possible all
2.3-2.380.411.7662121,292.9
2.38-2.480.3372.171651,298.5
2.48-2.590.2662.866841,298.2
2.59-2.730.2323.667421,297.4
2.73-2.90.1395.767811,298.2
2.9-3.120.0958.467301,298.1
3.12-3.430.05413.466231,297.5
3.43-3.930.03920.464711,296.4
3.93-4.930.0327.465661,298.2
4.93-28.30.02130.168891,297.4

-
Phasing

PhasingMethod: MAD

-
Processing

Software
NameVersionClassificationNB
MolProbity3beta29model building
SOLVEphasing
REFMAC5.2.0019refinement
XSCALEdata scaling
PDB_EXTRACT2data extraction
ADSCQUANTUMdata collection
XDSdata reduction
RefinementMethod to determine structure: MAD / Resolution: 2.3→28.273 Å / Cor.coef. Fo:Fc: 0.963 / Cor.coef. Fo:Fc free: 0.936 / SU B: 11.84 / SU ML: 0.145 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.193 / ESU R Free: 0.183 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: 1. ATOM RECORD CONTAINS RESIDUAL B FACTORS ONLY. 2. HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. 3. ANALYSIS OF THE DIFFRACTION DATA INDICATED HEMIHEDERAL TWINNING WITH A TWIN FRACTION ...Details: 1. ATOM RECORD CONTAINS RESIDUAL B FACTORS ONLY. 2. HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. 3. ANALYSIS OF THE DIFFRACTION DATA INDICATED HEMIHEDERAL TWINNING WITH A TWIN FRACTION OF 0.135 AND WITH A TWIN LAW OF K,H,-L. 4. THE INITIAL REFINEMENT WAS AGAINST THE NON-DETWINNED DATA AND INCLUDED PHASE RESTRAINTS TO THE EXPERIMENTAL MAD PHASES FROM ANOTHER CRYSTAL. 5. FOR THE FINAL STAGES OF REFINEMENT, THE DIFFRACTION INTENSITIES WERE DETWINNED USING THE CCP4 PROGAM DETWIN WITH A TWIN FRACTION OF 0.135 AND A TWIN OPERATION OF K,H,-L. 6. ETHYLENE GLYCOL USED AS A CRYOPROTECTANT AND NITRATE FROM THE CRYSTALLIZATION WERE MODELED INTO THE STRUCTURE. 7. ELECTRON DENSITIES FOR MSE 1-THR 14 AND THR 263-GLN 269 WERE DISORDERED, THEREFORE THESE RESIDUES WERE NOT MODELED. 8. 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. 9. ASP 233 IS A RAMACHANDRAN OUTLIER EVEN THOUGH IT IS MODELED INTO WELL-ORDERED ELECTRON DENSITY. 10. UNEXPLAINED NEGATIVE DIFFERENCE ELECTRON DENSITY IS OBSERVED BETWEEN LEU 203 AND LEU 211.
RfactorNum. reflection% reflectionSelection details
Rfree0.225 922 5.1 %RANDOM
Rwork0.173 ---
all0.175 ---
obs0.175 18113 98.39 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 60.7 Å2
Baniso -1Baniso -2Baniso -3
1-0.08 Å20.04 Å20 Å2
2--0.08 Å20 Å2
3----0.12 Å2
Refinement stepCycle: LAST / Resolution: 2.3→28.273 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1846 0 64 113 2023
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0221942
X-RAY DIFFRACTIONr_bond_other_d0.0020.021345
X-RAY DIFFRACTIONr_angle_refined_deg1.44922619
X-RAY DIFFRACTIONr_angle_other_deg0.92633287
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.0535251
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.57623.76869
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.49915308
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.8751513
X-RAY DIFFRACTIONr_chiral_restr0.0760.2311
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.022112
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02355
X-RAY DIFFRACTIONr_nbd_refined0.2170.2386
X-RAY DIFFRACTIONr_nbd_other0.2040.21543
X-RAY DIFFRACTIONr_nbtor_refined0.1740.2953
X-RAY DIFFRACTIONr_nbtor_other0.0880.21063
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1340.2118
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1670.215
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2540.253
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.110.29
X-RAY DIFFRACTIONr_mcbond_it1.74231281
X-RAY DIFFRACTIONr_mcbond_other0.3623497
X-RAY DIFFRACTIONr_mcangle_it2.89752013
X-RAY DIFFRACTIONr_scbond_it5.3668731
X-RAY DIFFRACTIONr_scangle_it6.95511604
LS refinement shellResolution: 2.3→2.362 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.307 57 -
Rwork0.252 1243 -
obs-1300 97.6 %
Refinement TLS params.Method: refined / Origin x: 38.473 Å / Origin y: 32.615 Å / Origin z: 18.843 Å
111213212223313233
T-0.3324 Å2-0.0486 Å2-0.0338 Å2--0.2195 Å20.0833 Å2---0.2596 Å2
L4.488 °2-2.4518 °2-0.9421 °2-3.0391 °20.6788 °2--1.4702 °2
S-0.0573 Å °-0.2827 Å °-0.4242 Å °-0.0967 Å °0.1212 Å °0.3692 Å °0.2482 Å °-0.1624 Å °-0.0639 Å °
Refinement TLS groupSelection: ALL

+
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