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- PDB-4gbj: Crystal structure of NAD-binding 6-phosphogluconate dehydrogenase... -

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Basic information

Entry
Database: PDB / ID: 4gbj
TitleCrystal structure of NAD-binding 6-phosphogluconate dehydrogenase from Dyadobacter fermentans
Components6-phosphogluconate dehydrogenase NAD-binding
KeywordsOXIDOREDUCTASE / Structural Genomics / PSI-Biology / Midwest Center for Structural Genomics / MCSG
Function / homology
Function and homology information


organic acid catabolic process / NAD binding / NADP binding / oxidoreductase activity
Similarity search - Function
3-hydroxyisobutyrate dehydrogenase-like, NAD-binding domain / NAD-binding of NADP-dependent 3-hydroxyisobutyrate dehydrogenase / : / 3-hydroxyisobutyrate dehydrogenase-related / 6-phosphogluconate dehydrogenase, NADP-binding / NAD binding domain of 6-phosphogluconate dehydrogenase / 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 ...3-hydroxyisobutyrate dehydrogenase-like, NAD-binding domain / NAD-binding of NADP-dependent 3-hydroxyisobutyrate dehydrogenase / : / 3-hydroxyisobutyrate dehydrogenase-related / 6-phosphogluconate dehydrogenase, NADP-binding / NAD binding domain of 6-phosphogluconate dehydrogenase / 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
6-phosphogluconate dehydrogenase NAD-binding
Similarity search - Component
Biological speciesDyadobacter fermentans (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.05 Å
AuthorsMichalska, K. / Holowicki, J. / Clancy, S. / Joachimiak, A. / Midwest Center for Structural Genomics (MCSG)
CitationJournal: To be Published
Title: Crystal structure of NAD-binding 6-phosphogluconate dehydrogenase from Dyadobacter fermentans
Authors: Michalska, K. / Holowicki, J. / Clancy, S. / Joachimiak, A. / Midwest Center for Structural Genomics (MCSG)
History
DepositionJul 27, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 5, 2012Provider: repository / Type: Initial release
Revision 1.1Nov 6, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / 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 / 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_seq_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_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.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_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

Downloads & links

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Assembly

Deposited unit
A: 6-phosphogluconate dehydrogenase NAD-binding
B: 6-phosphogluconate dehydrogenase NAD-binding
C: 6-phosphogluconate dehydrogenase NAD-binding
D: 6-phosphogluconate dehydrogenase NAD-binding
hetero molecules


Theoretical massNumber of molelcules
Total (without water)128,7738
Polymers128,6814
Non-polymers924
Water7,855436
1
B: 6-phosphogluconate dehydrogenase NAD-binding
hetero molecules

A: 6-phosphogluconate dehydrogenase NAD-binding


Theoretical massNumber of molelcules
Total (without water)64,3643
Polymers64,3412
Non-polymers231
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_456x-1/2,-y+1/2,-z+11
Buried area4920 Å2
ΔGint-70 kcal/mol
Surface area22010 Å2
MethodPISA
2
C: 6-phosphogluconate dehydrogenase NAD-binding
hetero molecules

D: 6-phosphogluconate dehydrogenase NAD-binding
hetero molecules


Theoretical massNumber of molelcules
Total (without water)64,4105
Polymers64,3412
Non-polymers693
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation1_455x-1,y,z1
Buried area5110 Å2
ΔGint-84 kcal/mol
Surface area21640 Å2
MethodPISA
3
A: 6-phosphogluconate dehydrogenase NAD-binding


Theoretical massNumber of molelcules
Total (without water)32,1701
Polymers32,1701
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
4
B: 6-phosphogluconate dehydrogenase NAD-binding
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,1932
Polymers32,1701
Non-polymers231
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
5
C: 6-phosphogluconate dehydrogenase NAD-binding
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,2163
Polymers32,1701
Non-polymers462
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
6
D: 6-phosphogluconate dehydrogenase NAD-binding
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,1932
Polymers32,1701
Non-polymers231
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)79.633, 89.645, 151.506
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
DetailsTHE AUTHOR STATES THAT THE BIOLOGICAL UNIT OF THIS PROTEIN IS UNKNOWN.

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Components

#1: Protein
6-phosphogluconate dehydrogenase NAD-binding


Mass: 32170.340 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Dyadobacter fermentans (bacteria) / Strain: DSM 18053 / Gene: Dfer_3638 / Plasmid: pMCSG57 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) Magic / References: UniProt: C6VV20
#2: Chemical
ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Na
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 436 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 2.1 Å3/Da / Density % sol: 41.46 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 0.1 M Bis-Tris/HCl pH 6.5, 25% PEG3350, VAPOR DIFFUSION, SITTING DROP, temperature 289K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.97931 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jul 14, 2012 / Details: mirrors
RadiationMonochromator: double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97931 Å / Relative weight: 1
ReflectionResolution: 2.05→50 Å / Num. all: 68406 / Num. obs: 68343 / % possible obs: 99.9 % / Observed criterion σ(I): -3 / Redundancy: 6.4 % / Biso Wilson estimate: 29.45 Å2 / Rmerge(I) obs: 0.107 / Net I/σ(I): 18.4
Reflection shellResolution: 2.05→2.09 Å / Redundancy: 6.3 % / Rmerge(I) obs: 0.75 / Mean I/σ(I) obs: 2.3 / % possible all: 99.8

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Processing

Software
NameVersionClassification
SBC-Collectdata collection
SHELXmodel building
MLPHAREphasing
DMmodel building
BUCCANEERmodel building
Cootmodel building
BUSTER2.10.0refinement
HKL-3000data reduction
HKL-3000data scaling
SHELXphasing
DMphasing
BUCCANEERphasing
RefinementMethod to determine structure: SAD / Resolution: 2.05→30.01 Å / Cor.coef. Fo:Fc: 0.946 / Cor.coef. Fo:Fc free: 0.9341 / Isotropic thermal model: isotropic / Cross valid method: THROUGHOUT / σ(F): 0
Details: HYDROGEN ATOMS HAVE BEEN ADDED AT THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.1973 1380 2.02 %thin resolution shells
Rwork0.1601 ---
obs0.1609 68270 99.32 %-
all-68270 --
Displacement parametersBiso mean: 41.47 Å2
Baniso -1Baniso -2Baniso -3
1-3.7956 Å20 Å20 Å2
2---9.0994 Å20 Å2
3---5.3038 Å2
Refine analyzeLuzzati coordinate error obs: 0.241 Å
Refinement stepCycle: LAST / Resolution: 2.05→30.01 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8706 0 4 436 9146
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.01217629HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.1131976HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d4900SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes213HARMONIC2
X-RAY DIFFRACTIONt_gen_planes2562HARMONIC5
X-RAY DIFFRACTIONt_it17629HARMONIC20
X-RAY DIFFRACTIONt_nbd6SEMIHARMONIC5
X-RAY DIFFRACTIONt_omega_torsion3.84
X-RAY DIFFRACTIONt_other_torsion2.96
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion1187SEMIHARMONIC5
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_contact19578SEMIHARMONIC4
LS refinement shellResolution: 2.05→2.1 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.2632 69 1.5 %
Rwork0.1905 4538 -
all0.1915 4607 -
obs--99.32 %
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)
102.839-2.81386.9481-1.57061.21140.0171-0.3399-0.4454-0.0297-0.0965-0.06410.2876-0.39690.0794-0.2631-0.09930.152-0.17550.1420.266640.857426.495468.2435
26.35760.9872-0.82351.96780.39072.7393-0.19520.5247-0.54420.059-0.08250.10150.2237-0.54420.2778-0.2552-0.05060.0828-0.0063-0.1136-0.059843.578538.027360.4906
32.5187-0.0394-0.50130.34550.23091.29080.0085-0.1313-0.14680.0518-0.0460.04170.0967-0.07020.0376-0.0364-0.00650.015-0.08510.0061-0.037671.340340.265864.3835
45.54952.812-0.56791.3857-0.48822.9924-0.0551-0.4911-0.20810.18340.07070.0930.3806-0.4121-0.01560.0245-0.0416-0.0128-0.03650.1003-0.007471.329831.165266.8302
51.6806-0.46090.8763.1517-0.332.2117-0.04480.0989-0.34280.13870.06440.23280.3523-0.2234-0.0195-0.0403-0.01220.0268-0.0723-0.0113-0.042867.299136.997950.2687
61.9289-1.26642.51612.3848-1.5321.7740.0505-0.0753-0.16160.05560.038-0.02730.53760.0057-0.08850.12820.02130.0179-0.0932-0.0162-0.009376.458228.477356.5991
70.54830.11121.15871.40772.83931.84060.02390.0257-0.1165-0.15090.00910.07140.0842-0.0754-0.033-0.0298-0.0420.04960.0056-0.06520.008655.3047-14.886770.7759
81.1681-1.33610.88785.65652.61910-0.01450.2688-0.5012-0.05890.01560.07560.2613-0.0933-0.0011-0.1127-0.10260.05020.1308-0.152-0.053455.684-19.335867.0604
95.1458-1.6207-1.2512.25890.45122.73750.05580.5119-0.158-0.1432-0.0954-0.04280.02150.08250.0396-0.1559-0.03130.01380.0353-0.006-0.175258.6125-5.966274.6362
102.14940.00910.09410.6394-0.01121.09940.00360.1926-0.0721-0.0822-0.01930.06320.1115-0.03330.0156-0.0318-0.0202-0.013-0.0625-0.015-0.035331.8203-3.738587.744
111.9247-1.2412-0.13260.016-0.76810.81830.15780.319-0.2935-0.0787-0.09420.03930.13330.1325-0.06360.00860.01860.0022-0.0083-0.0558-0.027640.5882-8.715988.9536
120.5495-0.25880.15782.01180.08291.47210.0591-0.025-0.12290.033-0.02110.05210.14580.0867-0.038-0.0041-0.0011-0.0063-0.03990.00280.006437.2088-11.424597.4308
136.39182.91042.91043.50892.91043.45520.1294-0.45710.38490.4468-0.20830.0446-0.21620.4360.0789-0.1563-0.1520.02970.1807-0.0911-0.18625.2884-2.9764.1574
145.24942.1144-1.28613.2038-0.60950.92460.107-0.5442-0.04940.0104-0.3139-0.36610.03060.54420.2069-0.21860.0613-0.0130.18910.0469-0.184228.1719-11.36356.8659
155.75580.35-0.14612.8866-0.55325.3250.2331-0.45140.228-0.0556-0.27540.21960.18950.54420.0423-0.14050.00840.0041-0.0833-0.0264-0.148316.1202-13.288158.9274
161.086-0.50071.02740.9949-0.95141.4873-0.1654-0.22350.08380.23920.1547-0.0716-0.1065-0.13860.0106-0.01260.02260.0147-0.0448-0.0041-0.0682-0.28511.769646.6649
172.4257-0.78960.04230.7196-0.38481.2796-0.2266-0.53240.03980.11370.177-0.1081-0.05010.13360.0496-0.04940.0126-0.02730.0506-0.0082-0.09729.43752.727141.9099
180.6492-1.354-2.16652.7264-0.08643.57210.0737-0.35390.26430.05980.0167-0.1319-0.33160.3369-0.09050.0172-0.0347-0.0238-0.0196-0.0466-0.03347.889112.869439.3876
192.92151.8353-0.45771.55890.22232.1773-0.0088-0.10020.2769-0.1273-0.10230.23770.0072-0.54420.1111-0.22680.00370.03450.1732-0.0122-0.125744.60116.019841.1807
204.2070.684-1.37391.20492.21371.99490.0071-0.12760.0874-0.0288-0.17620.1474-0.196-0.3140.1691-0.11240.02370.03130.0643-0.0222-0.089153.009510.313442.2105
212.520.9326-0.14541.37630.29023.03590.0891-0.40760.27970.2069-0.08180.0975-0.1722-0.5442-0.0072-0.09670.05720.06010.084-0.0166-0.089956.299410.444149.7951
220.0006-0.03820.98350.2061-0.49291.1095-0.0641-0.2051-0.03170.09890.21160.01530.0374-0.3931-0.1475-0.00640.01370.02620.01460.0503-0.021376.6219-8.409446.2733
232.9638-0.3029-1.190801.05320.17290.042-0.1895-0.10640.2671-0.02110.09620.0992-0.2554-0.0209-0.0686-0.06170.02490.05940.11860.033765.3406-13.342942.4966
241.11990.315-0.09170.9304-0.35611.341-0.0069-0.0738-0.0890.04060.08180.06330.0891-0.2233-0.0749-0.0319-0.02310.00940.00180.034-0.026469.6964-4.279932.0432
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1{A|1 - A|52}A1 - 52
2X-RAY DIFFRACTION2{A|53 - A|155}A53 - 155
3X-RAY DIFFRACTION3{A|156 - A|210}A156 - 210
4X-RAY DIFFRACTION4{A|211 - A|234}A211 - 234
5X-RAY DIFFRACTION5{A|235 - A|274}A235 - 274
6X-RAY DIFFRACTION6{A|275 - A|293}A275 - 293
7X-RAY DIFFRACTION7{B|4 - B|16}B4 - 16
8X-RAY DIFFRACTION8{B|17 - B|47}B17 - 47
9X-RAY DIFFRACTION9{B|48 - B|161}B48 - 161
10X-RAY DIFFRACTION10{B|162 - B|212}B162 - 212
11X-RAY DIFFRACTION11{B|213 - B|255}B213 - 255
12X-RAY DIFFRACTION12{B|256 - B|293}B256 - 293
13X-RAY DIFFRACTION13{C|3 - C|41}C3 - 41
14X-RAY DIFFRACTION14{C|42 - C|101}C42 - 101
15X-RAY DIFFRACTION15{C|102 - C|157}C102 - 157
16X-RAY DIFFRACTION16{C|158 - C|212}C158 - 212
17X-RAY DIFFRACTION17{C|213 - C|274}C213 - 274
18X-RAY DIFFRACTION18{C|275 - C|294}C275 - 294
19X-RAY DIFFRACTION19{D|4 - D|108}D4 - 108
20X-RAY DIFFRACTION20{D|109 - D|125}D109 - 125
21X-RAY DIFFRACTION21{D|126 - D|171}D126 - 171
22X-RAY DIFFRACTION22{D|172 - D|220}D172 - 220
23X-RAY DIFFRACTION23{D|221 - D|234}D221 - 234
24X-RAY DIFFRACTION24{D|235 - D|293}D235 - 293

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