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- PDB-2yfq: Crystal structure of Glutamate dehydrogenase from Peptoniphilus a... -

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Basic information

Entry
Database: PDB / ID: 2yfq
TitleCrystal structure of Glutamate dehydrogenase from Peptoniphilus asaccharolyticus
ComponentsNAD-SPECIFIC GLUTAMATE DEHYDROGENASE
KeywordsOXIDOREDUCTASE
Function / homology
Function and homology information


glutamate catabolic process via 2-hydroxyglutarate / glutamate dehydrogenase / : / glutamate dehydrogenase (NAD+) activity / amino acid metabolic process
Similarity search - Function
Helicase, Ruva Protein; domain 3 - #1210 / Glutamate dehydrogenase / Leucine Dehydrogenase, chain A, domain 1 / NAD(P) binding domain of glutamate dehydrogenase / Leu/Phe/Val dehydrogenases active site / Glu / Leu / Phe / Val dehydrogenases active site. / Glutamate/phenylalanine/leucine/valine dehydrogenase / Glutamate/phenylalanine/leucine/valine dehydrogenase, dimerisation domain / Glu/Leu/Phe/Val dehydrogenase, dimerisation domain / Glutamate/Leucine/Phenylalanine/Valine dehydrogenase ...Helicase, Ruva Protein; domain 3 - #1210 / Glutamate dehydrogenase / Leucine Dehydrogenase, chain A, domain 1 / NAD(P) binding domain of glutamate dehydrogenase / Leu/Phe/Val dehydrogenases active site / Glu / Leu / Phe / Val dehydrogenases active site. / Glutamate/phenylalanine/leucine/valine dehydrogenase / Glutamate/phenylalanine/leucine/valine dehydrogenase, dimerisation domain / Glu/Leu/Phe/Val dehydrogenase, dimerisation domain / Glutamate/Leucine/Phenylalanine/Valine dehydrogenase / Glutamate/phenylalanine/leucine/valine dehydrogenase, C-terminal / Glutamate/Leucine/Phenylalanine/Valine dehydrogenase / Helicase, Ruva Protein; domain 3 / 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-specific glutamate dehydrogenase
Similarity search - Component
Biological speciesPEPTONIPHILUS ASACCHAROLYTICUS (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.94 Å
AuthorsOliveira, T. / Panjikar, S. / Carrigan, J.B. / Sharkey, M.A. / Hamza, M. / Engel, P.C. / Khan, A.R.
CitationJournal: J.Struct.Biol. / Year: 2012
Title: Crystal Structure of Nad-Dependent Peptoniphilus Asaccharolyticus Glutamate Dehydrogenase Reveals Determinants of Cofactor Specificity.
Authors: Oliveira, T. / Panjikar, S. / Carrigan, J.B. / Hamza, M. / Engel, P.C. / Khan, A.R.
History
DepositionApr 7, 2011Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 23, 2011Provider: repository / Type: Initial release
Revision 1.1Feb 29, 2012Group: Other
Revision 1.2May 8, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / struct_ncs_dom_lim / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id / _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: NAD-SPECIFIC GLUTAMATE DEHYDROGENASE
B: NAD-SPECIFIC GLUTAMATE DEHYDROGENASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)93,5146
Polymers93,1302
Non-polymers3844
Water1086
1
A: NAD-SPECIFIC GLUTAMATE DEHYDROGENASE
B: NAD-SPECIFIC GLUTAMATE DEHYDROGENASE
hetero molecules

A: NAD-SPECIFIC GLUTAMATE DEHYDROGENASE
B: NAD-SPECIFIC GLUTAMATE DEHYDROGENASE
hetero molecules

A: NAD-SPECIFIC GLUTAMATE DEHYDROGENASE
B: NAD-SPECIFIC GLUTAMATE DEHYDROGENASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)280,54118
Polymers279,3896
Non-polymers1,15312
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_555-x+y,-x,z1
crystal symmetry operation2_555-y,x-y,z1
Buried area23540 Å2
ΔGint-226.3 kcal/mol
Surface area88180 Å2
MethodPISA
Unit cell
Length a, b, c (Å)153.314, 153.314, 318.993
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number155
Space group name H-MH32
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B

NCS domain segments:

Ens-ID: 1 / Refine code: 2

Dom-IDComponent-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11ALAALAVALVALAA18 - 19518 - 195
21ALAALAVALVALBB18 - 19518 - 195
12ARGARGGLNGLNAA200 - 218200 - 218
22ARGARGGLNGLNBB200 - 218200 - 218
13PHEPHEASNASNAA226 - 247226 - 247
23PHEPHEASNASNBB226 - 247226 - 247
14ALAALAGLYGLYAA315 - 324315 - 324
24ALAALAGLYGLYBB315 - 324315 - 324
15GLYGLYARGARGAA330 - 418330 - 418
25GLYGLYARGARGBB330 - 418330 - 418

NCS oper: (Code: given
Matrix: (-0.5389, 0.8423, -0.004902), (0.8423, 0.539, 0.01035), (0.01136, 0.001447, -0.9999)
Vector: 0.2691, -0.6707, 158.9)

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Components

#1: Protein NAD-SPECIFIC GLUTAMATE DEHYDROGENASE / PADGH / NAD-GDH


Mass: 46564.758 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) PEPTONIPHILUS ASACCHAROLYTICUS (bacteria)
Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P28997, glutamate dehydrogenase
#2: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 6 / Source method: isolated from a natural source / Formula: H2O

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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: 3.82 Å3/Da / Density % sol: 67.8 % / Description: NONE
Crystal growpH: 7 / Details: 0.1 M SODIUM CACODYLATE PH 6.5, 200 MM NACL

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: BM14 / Wavelength: 0.97862
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Feb 15, 2009
RadiationMonochromator: SI111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97862 Å / Relative weight: 1
ReflectionResolution: 2.94→50 Å / Num. obs: 58934 / % possible obs: 99.8 % / Observed criterion σ(I): -3 / Redundancy: 11.5 % / Biso Wilson estimate: 72.9 Å2 / Rmerge(I) obs: 0.12 / Net I/σ(I): 18.7
Reflection shellResolution: 2.94→3.01 Å / Redundancy: 8.3 % / Rmerge(I) obs: 0.59 / Mean I/σ(I) obs: 2.9 / % possible all: 97.8

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Processing

Software
NameVersionClassification
REFMAC5.5.0109refinement
HKL-2000data reduction
SCALEPACKdata scaling
Auto-Rickshawphasing
RefinementMethod to determine structure: SAD
Starting model: NONE

Resolution: 2.94→20 Å / Cor.coef. Fo:Fc: 0.928 / Cor.coef. Fo:Fc free: 0.902 / SU B: 36.004 / SU ML: 0.325 / Cross valid method: THROUGHOUT / ESU R: 0.831 / ESU R Free: 0.394 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.28693 1015 3.4 %RANDOM
Rwork0.24235 ---
obs0.24389 29106 97.78 %-
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 mean: 79.616 Å2
Baniso -1Baniso -2Baniso -3
1--0.41 Å20.21 Å20 Å2
2---0.41 Å20 Å2
3---0.62 Å2
Refinement stepCycle: LAST / Resolution: 2.94→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6082 0 20 6 6108
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0226216
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.4391.968412
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.945788
X-RAY DIFFRACTIONr_dihedral_angle_2_deg40.42224.764275
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.666151053
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.7731534
X-RAY DIFFRACTIONr_chiral_restr0.1010.2913
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0214710
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.4431.53900
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it0.7552.56232
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it1.4252316
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it2.274102180
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

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

Dom-IDAuth asym-IDNumberTypeRms dev position (Å)Weight position
1A1272tight positional0.030.05
2B1272tight positional0.030.05
1A1188medium positional0.090.5
2B1188medium positional0.090.5
1A1272tight thermal0.211.5
2B1272tight thermal0.211.5
1A1188medium thermal0.412.5
2B1188medium thermal0.412.5
LS refinement shellResolution: 2.943→3.018 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.388 68 -
Rwork0.309 1955 -
obs--92.08 %
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)
13.1898-0.4041.24171.9071-0.31914.00030.14650.30920.5929-0.16270.0021-0.3267-1.11160.8186-0.14870.5437-0.27190.25690.3024-0.08310.478113.757222.281668.7998
21.96540.9140.07371.4281-0.65823.7620.18870.12520.0833-0.15120.1095-0.2302-0.30960.9295-0.29820.1591-0.13120.13470.3409-0.14670.345515.88537.183765.0838
327.377-12.55152.33738.2726-7.707417.68941.17091.982-0.7914-0.0603-1.57410.1051-1.43341.45440.40321.2734-0.88250.22141.17420.03750.54916.788922.653536.9153
42.41261.7385-1.50784.3966-2.17784.13840.09610.53170.4386-0.016-0.0387-0.316-1.26021.2827-0.05740.7717-0.57640.14870.97990.10490.491922.170725.341843.4592
51.10520.8498-0.34461.2159-0.36153.5440.05180.52040.3372-0.20050.312-0.0003-1.09410.1624-0.36380.5714-0.03580.11530.34340.11040.4312.734418.777550.5938
63.0302-0.39131.45682.5418-0.74934.2384-0.0486-0.32540.68670.27180.1914-0.3828-1.36180.479-0.14280.6826-0.2340.21970.2519-0.22390.489911.401923.693790.2677
70.84290.8885-0.10082.11740.15964.75750.261-0.22090.17710.24260.23420.0011-1.1148-0.1862-0.49520.44410.03110.19110.2748-0.07940.3593-2.561717.178293.9849
830.4756-3.6147-8.14761.2644-1.851711.85570.9492-4.4533-0.98180.34630.19230.6334-1.76072.4181-1.14152.332-0.82120.49231.2509-0.49050.738610.091126.1205122.2861
92.27071.94741.38985.59591.96963.30450.1144-0.3390.7170.72780.0257-0.0436-1.01410.2518-0.14011.3482-0.17050.12460.5622-0.30670.627410.130633.6437117.0602
102.75170.5788-0.86981.0799-0.43283.49530.1872-0.76210.17950.51660.1173-0.3153-0.56850.6991-0.30450.4766-0.0926-0.01660.475-0.21440.439713.048712.1132107.8091
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A6 - 119
2X-RAY DIFFRACTION2A120 - 199
3X-RAY DIFFRACTION3A200 - 227
4X-RAY DIFFRACTION4A228 - 360
5X-RAY DIFFRACTION5A361 - 418
6X-RAY DIFFRACTION6B5 - 119
7X-RAY DIFFRACTION7B120 - 199
8X-RAY DIFFRACTION8B200 - 227
9X-RAY DIFFRACTION9B228 - 354
10X-RAY DIFFRACTION10B355 - 418

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