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- PDB-3dfu: CRYSTAL STRUCTURE OF A PUTATIVE ROSSMANN-LIKE DEHYDROGENASE (CGL2... -

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Basic information

Entry
Database: PDB / ID: 3dfu
TitleCRYSTAL STRUCTURE OF A PUTATIVE ROSSMANN-LIKE DEHYDROGENASE (CGL2689) FROM CORYNEBACTERIUM GLUTAMICUM AT 2.07 A RESOLUTION
ComponentsUncharacterized Protein from 6-Phosphogluconate Dehydrogenase-Like Family
KeywordsOXIDOREDUCTASE / PUTATIVE ROSSMANN-LIKE DEHYDROGENASE / STRUCTURAL GENOMICS / JOINT CENTER FOR STRUCTURAL GENOMICS / JCSG / PROTEIN STRUCTURE INITIATIVE / PSI-2
Function / homology
Function and homology information


N-(1-d-carboxylethyl)-l-norvaline Dehydrogenase; domain 2 - #40 / : / Rossmann-like domain / 6-phosphogluconate dehydrogenase C-terminal domain-like / N-(1-d-carboxylethyl)-l-norvaline Dehydrogenase; domain 2 / NAD(P)-binding Rossmann-like Domain / Rossmann fold / Orthogonal Bundle / 3-Layer(aba) Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
CGL2689-like C-terminal domain-containing protein
Similarity search - Component
Biological speciesCorynebacterium glutamicum (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.07 Å
AuthorsJoint Center for Structural Genomics (JCSG)
CitationJournal: To be published
Title: Crystal structure of Protein of Unknown Function from the 6-Phosphogluconate Dehydrogenase-Like Family (NP_601885.1) from CORYNEBACTERIUM GLUTAMICUM ATCC 13032 KITASATO at 2.07 A resolution
Authors: Joint Center for Structural Genomics (JCSG)
History
DepositionJun 12, 2008Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 1, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2Oct 25, 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 / Refinement description / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_entry_details / pdbx_modification_feature / struct_ncs_dom_lim
Item: _pdbx_entry_details.has_protein_modification / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.end_auth_comp_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Uncharacterized Protein from 6-Phosphogluconate Dehydrogenase-Like Family
B: Uncharacterized Protein from 6-Phosphogluconate Dehydrogenase-Like Family
hetero molecules


Theoretical massNumber of molelcules
Total (without water)51,6523
Polymers51,5602
Non-polymers921
Water4,486249
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6030 Å2
ΔGint-40 kcal/mol
Surface area20350 Å2
MethodPISA
Unit cell
Length a, b, c (Å)155.790, 47.070, 63.240
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP21212
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B

NCS domain segments:

Component-ID: 1 / Ens-ID: 1 / Beg auth comp-ID: PRO / Beg label comp-ID: PRO / End auth comp-ID: GLN / End label comp-ID: GLN / Refine code: 6 / Auth seq-ID: 4 - 227 / Label seq-ID: 5 - 228

Dom-IDAuth asym-IDLabel asym-ID
1AA
2BB
DetailsAUTHORS STATE THAT CRYSTAL PACKING ANALYSIS SUPPORTS THE ASSIGNMENT OF A DIMER AS THE SIGNIFICANT OLIGOMERIZATION STATE.

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Components

#1: Protein Uncharacterized Protein from 6-Phosphogluconate Dehydrogenase-Like Family


Mass: 25779.957 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Corynebacterium glutamicum (bacteria) / Gene: NP_601885.1, Cgl2689, cg2976 / Plasmid: SpeedET / Production host: Escherichia coli (E. coli) / Strain (production host): HK100 / References: UniProt: Q8NM90
#2: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 249 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY
Sequence detailsTHE CONSTRUCT WAS EXPRESSED WITH A PURIFICATION TAG MGSDKIHHHHHHENLYFQG. THE TAG WAS REMOVED WITH ...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.

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Experimental details

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Experiment

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

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Sample preparation

CrystalDensity Matthews: 2.25 Å3/Da / Density % sol: 45.3 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 6
Details: 20.0% polyethylene glycol 6000, 1.0M lithium chloride, 0.1M MES pH 6.0, NANODROP, VAPOR DIFFUSION, SITTING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL11-1 / Wavelength: 0.91837,0.97960,0.97905
DetectorType: MARMOSAIC 325 mm CCD / Detector: CCD / Date: May 14, 2008 / 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
10.918371
20.97961
30.979051
ReflectionResolution: 2.07→27.951 Å / Num. obs: 29174 / % possible obs: 98.7 % / Observed criterion σ(I): -3 / Biso Wilson estimate: 30.352 Å2 / Rmerge(I) obs: 0.047 / Net I/σ(I): 12.28
Reflection shell

Diffraction-ID: 1

Resolution (Å)Highest resolution (Å)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. unique obs% possible all
2.07-2.140.4332.29976519098.7
2.14-2.230.306310891566398.9
2.23-2.330.2363.910393538399
2.33-2.450.1774.910298533199.3
2.45-2.610.1326.511035570199
2.61-2.810.0968.710430539799
2.81-3.090.06412.110403536199
3.09-3.530.0371910435537998.8
3.53-4.440.02328.510657544498.6
4.440.0183410767543397

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Phasing

PhasingMethod: MAD

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Processing

Software
NameVersionClassificationNB
REFMAC5.2.0019refinement
PHENIXrefinement
SHELXphasing
MolProbity3beta29model building
XSCALEdata scaling
PDB_EXTRACT3.004data extraction
XDSdata reduction
SHELXDphasing
autoSHARPphasing
RefinementMethod to determine structure: MAD / Resolution: 2.07→27.951 Å / Cor.coef. Fo:Fc: 0.954 / Cor.coef. Fo:Fc free: 0.933 / SU B: 9.323 / SU ML: 0.128 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.221 / ESU R Free: 0.174
Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES
Details: 1. HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. 2. ATOM RECORDS CONTAIN 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 RECORDS CONTAIN 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 FOR THE REDUCED SCATTERING POWER DUE TO PARTIAL S-MET INCORPORATION. 4. GOL MOLECULE FROM THE CRYO SOLUTION IS MODELED.
RfactorNum. reflection% reflectionSelection details
Rfree0.223 1479 5.1 %RANDOM
Rwork0.191 ---
obs0.193 29123 99.43 %-
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: 31.66 Å2
Baniso -1Baniso -2Baniso -3
1--1.74 Å20 Å20 Å2
2--2 Å20 Å2
3----0.26 Å2
Refinement stepCycle: LAST / Resolution: 2.07→27.951 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3445 0 6 249 3700
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.0223590
X-RAY DIFFRACTIONr_bond_other_d0.0030.022340
X-RAY DIFFRACTIONr_angle_refined_deg1.5251.9574891
X-RAY DIFFRACTIONr_angle_other_deg1.38335731
X-RAY DIFFRACTIONr_dihedral_angle_1_deg3.5615476
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.51324.573164
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.26515587
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.731522
X-RAY DIFFRACTIONr_chiral_restr0.0930.2567
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.024094
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02716
X-RAY DIFFRACTIONr_nbd_refined0.1750.2686
X-RAY DIFFRACTIONr_nbd_other0.1430.22293
X-RAY DIFFRACTIONr_nbtor_refined0.1480.21764
X-RAY DIFFRACTIONr_nbtor_other0.0730.21737
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.0950.2219
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.0660.27
X-RAY DIFFRACTIONr_symmetry_vdw_other0.1490.237
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.0350.28
X-RAY DIFFRACTIONr_mcbond_it1.13822723
X-RAY DIFFRACTIONr_mcbond_other0.1632944
X-RAY DIFFRACTIONr_mcangle_it1.68943679
X-RAY DIFFRACTIONr_scbond_it3.2961396
X-RAY DIFFRACTIONr_scangle_it4.29181200
Refine LS restraints NCS

Dom-ID: 1 / Auth asym-ID: A / Ens-ID: 1 / Number: 2703 / Refine-ID: X-RAY DIFFRACTION

TypeRms dev position (Å)Weight position
LOOSE POSITIONAL0.755
LOOSE THERMAL2.2610
LS refinement shellResolution: 2.068→2.122 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.252 104 -
Rwork0.239 2020 -
all-2124 -
obs--99.53 %
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)
12.25220.7651-1.22250.4799-0.44440.92680.0322-0.0158-0.11570.0221-0.0221-0.0490.03030.0508-0.0101-0.080.0145-0.0429-0.1154-0.0153-0.1098130.38210.738.069
24.4106-1.9413-1.53491.55230.94271.3433-0.281-0.2021-0.38410.18410.06770.29160.04570.01010.2133-0.01830.01040.0039-0.09660.0488-0.0764103.42410.2355.726
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA2 - 2293 - 230
2X-RAY DIFFRACTION2BB1 - 2282 - 229

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