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- PDB-3qsg: Crystal structure of NAD-binding phosphogluconate dehydrogenase-l... -

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Basic information

Entry
Database: PDB / ID: 3qsg
TitleCrystal structure of NAD-binding phosphogluconate dehydrogenase-like protein from Alicyclobacillus acidocaldarius
ComponentsNAD-binding phosphogluconate dehydrogenase-like protein
KeywordsStructural genomics / Unknown function / PSI-Biology / Midwest Center for Structural Genomics / MCSG / Rossmann-fold NAD-binding proteins
Function / homology
Function and homology information


oxidoreductase activity
Similarity search - Function
Phosphogluconate dehydrogenase, NAD-binding, putative, C-terminal / Domain of unknown function (DUF1932) / Pyrroline-5-carboxylate reductase, catalytic, N-terminal / NADP oxidoreductase coenzyme F420-dependent / N-(1-d-carboxylethyl)-l-norvaline Dehydrogenase; domain 2 / N-(1-d-carboxylethyl)-l-norvaline Dehydrogenase; domain 2 / 6-phosphogluconate dehydrogenase, domain 2 / 6-phosphogluconate dehydrogenase-like, C-terminal domain superfamily / NAD(P)-binding Rossmann-like Domain / NAD(P)-binding domain superfamily ...Phosphogluconate dehydrogenase, NAD-binding, putative, C-terminal / Domain of unknown function (DUF1932) / Pyrroline-5-carboxylate reductase, catalytic, N-terminal / NADP oxidoreductase coenzyme F420-dependent / N-(1-d-carboxylethyl)-l-norvaline Dehydrogenase; domain 2 / N-(1-d-carboxylethyl)-l-norvaline Dehydrogenase; domain 2 / 6-phosphogluconate dehydrogenase, domain 2 / 6-phosphogluconate dehydrogenase-like, C-terminal domain superfamily / NAD(P)-binding Rossmann-like Domain / NAD(P)-binding domain superfamily / Rossmann fold / Orthogonal Bundle / 3-Layer(aba) Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
NAD-binding phsophogluconase dehydrogenase-like protein
Similarity search - Component
Biological speciesAlicyclobacillus acidocaldarius subsp. acidocaldarius (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsMichalska, K. / Wu, R. / Bearden, J. / Joachimiak, A. / Midwest Center for Structural Genomics (MCSG)
CitationJournal: To be Published
Title: Crystal structure of NAD-binding phosphogluconate dehydrogenase-like protein from Alicyclobacillus acidocaldarius
Authors: Michalska, K. / Wu, R. / Bearden, J. / Joachimiak, A.
History
DepositionFeb 21, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 13, 2011Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Apr 3, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: NAD-binding phosphogluconate dehydrogenase-like protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,5653
Polymers33,4941
Non-polymers712
Water1,33374
1
A: NAD-binding phosphogluconate dehydrogenase-like protein
hetero molecules

A: NAD-binding phosphogluconate dehydrogenase-like protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)67,1306
Polymers66,9882
Non-polymers1424
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,y,-z1
Buried area5510 Å2
ΔGint-81 kcal/mol
Surface area22820 Å2
MethodPISA
Unit cell
Length a, b, c (Å)113.838, 61.005, 50.068
Angle α, β, γ (deg.)90.00, 112.16, 90.00
Int Tables number5
Space group name H-MC121
DetailsTHE AUTHOR STATES THAT THE BIOLOGICAL UNIT OF THIS PROTEIN IS UNKNOWN.

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Components

#1: Protein NAD-binding phosphogluconate dehydrogenase-like protein


Mass: 33494.160 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Alicyclobacillus acidocaldarius subsp. acidocaldarius (bacteria)
Strain: DSM 446 / Gene: Aaci_1610 / Plasmid: pMCSG7 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 Magic / References: UniProt: C8WX00
#2: Chemical ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 74 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.4 Å3/Da / Density % sol: 48.83 %
Crystal growTemperature: 297 K / Method: vapor diffusion, sitting drop / pH: 8
Details: 12% PEG6K, 2 M NaCl, pH 8, VAPOR DIFFUSION, SITTING DROP, temperature 297K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.97926 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Nov 10, 2010 / Details: mirrors
RadiationMonochromator: double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97926 Å / Relative weight: 1
ReflectionResolution: 1.9→50 Å / Num. all: 25141 / Num. obs: 25034 / % possible obs: 99.6 % / Observed criterion σ(I): -3 / Redundancy: 3.7 % / Biso Wilson estimate: 35.41 Å2 / Rmerge(I) obs: 0.065 / Net I/σ(I): 25.1
Reflection shellResolution: 1.9→1.93 Å / Redundancy: 3.5 % / Rmerge(I) obs: 0.421 / Mean I/σ(I) obs: 2.5 / % possible all: 99.4

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Processing

Software
NameVersionClassification
SBC-Collectdata collection
PHASERphasing
PHENIXrefinement
BUSTER2.8.0refinement
HKL-3000data reduction
HKL-3000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: different crystal form of the same protein (solved by SAD)

Resolution: 1.9→21.99 Å / Cor.coef. Fo:Fc: 0.9518 / Cor.coef. Fo:Fc free: 0.9454 / Isotropic thermal model: isotropic / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.201 1271 5.08 %RANDOM
Rwork0.185 ---
obs0.1859 25015 --
all-25015 --
Displacement parametersBiso mean: 49.09 Å2
Baniso -1Baniso -2Baniso -3
1-3.6729 Å20 Å2-1.5544 Å2
2--4.485 Å20 Å2
3----8.1579 Å2
Refine analyzeLuzzati coordinate error obs: 0.275 Å
Refinement stepCycle: LAST / Resolution: 1.9→21.99 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2095 0 2 74 2171
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.0122146HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.092911HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d734SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes44HARMONIC2
X-RAY DIFFRACTIONt_gen_planes332HARMONIC5
X-RAY DIFFRACTIONt_it2146HARMONIC20
X-RAY DIFFRACTIONt_nbd0SEMIHARMONIC5
X-RAY DIFFRACTIONt_omega_torsion3.3
X-RAY DIFFRACTIONt_other_torsion16.47
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion276SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact2521SEMIHARMONIC4
LS refinement shellResolution: 1.9→1.98 Å / Total num. of bins used: 13
RfactorNum. reflection% reflection
Rfree0.2286 128 4.61 %
Rwork0.1985 2650 -
all0.1998 2778 -
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)
12.2555-2.18592.62650.7054-1.38935.2078-0.0057-0.29650.03620.7017-0.0729-0.28010.07570.2380.07860.1064-0.0008-0.1724-0.1910.00820.024531.274816.234915.9574
24.74232.19783.32143.4903-0.07526.27130.0027-0.67810.09170.567-0.0274-0.3467-0.06750.27970.0247-0.07050.0057-0.3045-0.304-0.01950.11835.253523.819619.709
32.173-0.60670.14785.446-0.23171.3652-0.0584-0.00760.02210.2276-0.0413-0.4949-0.0860.04280.0997-0.1597-0.0041-0.0232-0.15010.00180.111130.474621.182.7378
46.206-0.947-1.751800.5941.4625-0.1276-0.6445-0.70110.11760.02890.01330.15380.13970.0987-0.0620.0154-0.007-0.09060.08070.0786-0.701616.60326.1986
55.7110.0867-2.31430.4630.49742.11950.2346-0.68710.42740.1466-0.0018-0.1448-0.12710.26-0.2328-0.1685-0.0254-0.0116-0.0797-0.04770.0066.341330.08275.6762
6-0.2369-3.1057-0.35280.595-0.09053.16040.0178-0.3369-0.06190.3546-0.14480.04670.2002-0.13150.127-0.1183-0.0813-0.04520.13510.0746-0.2986-6.208321.38119.991
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1{A|1 - A|23}A1 - 23
2X-RAY DIFFRACTION2{A|24 - A|61}A24 - 61
3X-RAY DIFFRACTION3{A|62 - A|163}A62 - 163
4X-RAY DIFFRACTION4{A|164 - A|224}A164 - 224
5X-RAY DIFFRACTION5{A|231 - A|271}A231 - 271
6X-RAY DIFFRACTION6{A|274 - A|285}A274 - 285

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