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- PDB-3k8z: Crystal Structure of Gudb1 a decryptified secondary glutamate deh... -

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Basic information

Entry
Database: PDB / ID: 3k8z
TitleCrystal Structure of Gudb1 a decryptified secondary glutamate dehydrogenase from B. subtilis
ComponentsNAD-specific glutamate dehydrogenase
KeywordsOXIDOREDUCTASE / GudB / Glutamate dehydrogenase / NAD
Function / homology
Function and homology information


glutamate dehydrogenase / glutamate catabolic process / : / 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
Cryptic catabolic NAD-specific glutamate dehydrogenase GudB
Similarity search - Component
Biological speciesBacillus subtilis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.4 Å
AuthorsGunka, K. / Newman, J.A. / Commichau, F.M. / Herzberg, C. / Rodrigues, C. / Hewitt, L. / Lewis, R.J. / Stulke, J.
CitationJournal: J.Mol.Biol. / Year: 2010
Title: Functional dissection of a trigger enzyme: mutations of the bacillus subtilis glutamate dehydrogenase RocG that affect differentially its catalytic activity and regulatory properties
Authors: Gunka, K. / Newman, J.A. / Commichau, F.M. / Herzberg, C. / Rodrigues, C. / Hewitt, L. / Lewis, R.J. / Stulke, J.
History
DepositionOct 15, 2009Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Jun 2, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Jan 22, 2014Group: Database references
Revision 1.3Mar 20, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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

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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
C: NAD-specific glutamate dehydrogenase
D: NAD-specific glutamate dehydrogenase
E: NAD-specific glutamate dehydrogenase
F: NAD-specific glutamate dehydrogenase


Theoretical massNumber of molelcules
Total (without water)281,8366
Polymers281,8366
Non-polymers00
Water8,953497
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)85.220, 192.491, 89.387
Angle α, β, γ (deg.)90.000, 118.740, 90.000
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11C
21D
12A
22B
32E
42F

NCS domain segments:
Dom-IDComponent-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
111VALVALILEILEchain C and (resseq 17:423 )CC17 - 42317 - 423
211VALVALILEILEchain D and (resseq 17:423 )DD17 - 42317 - 423
112VALVALASPASPchain A and (resseq 17:265 or resseq 295:423 )AA17 - 26517 - 265
122CYSCYSILEILEchain A and (resseq 17:265 or resseq 295:423 )AA295 - 423295 - 423
212VALVALASPASPchain B and (resseq 17:265 or resseq 295:423 )BB17 - 26517 - 265
222CYSCYSILEILEchain B and (resseq 17:265 or resseq 295:423 )BB295 - 423295 - 423
312VALVALASPASPchain E and (resseq 17:265 or resseq 295:423 )EE17 - 26517 - 265
322CYSCYSILEILEchain E and (resseq 17:265 or resseq 295:423 )EE295 - 423295 - 423
412VALVALASPASPchain F and (resseq 17:265 or resseq 295:423 )FF17 - 26517 - 265
422CYSCYSILEILEchain F and (resseq 17:265 or resseq 295:423 )FF295 - 423295 - 423

NCS ensembles :
ID
1
2

NCS oper:
IDCodeMatrixVector
1given(0.999999, -0.001716, 0.000176), (-0.001716, -0.999998, -0.001098), (0.000178, 0.001098, -0.999999)-0.010715, 14.3507, 77.403198
2given(-0.503549, -0.070518, 0.861084), (-0.049787, -0.992639, -0.110406), (0.862531, -0.098466, 0.496331)-42.504799, 18.439899, 25.8346
3given(1, 0.000438, 0.000213), (0.000436, -0.999958, 0.0092), (0.000217, -0.0092, -0.999958)0.01041, 13.7799, 77.4086
4given(-0.506968, 0.076813, -0.858535), (-0.047162, 0.992058, 0.116608), (0.860673, 0.099607, -0.499319)22.907101, -4.50956, 62.927799

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Components

#1: Protein
NAD-specific glutamate dehydrogenase / NAD-GDH


Mass: 46972.590 Da / Num. of mol.: 6 / Mutation: UNP residues V94 K95 A96 deletion
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus subtilis (bacteria) / Production host: Escherichia coli (E. coli) / References: UniProt: P50735, glutamate dehydrogenase
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 497 / Source method: isolated from a natural source / Formula: H2O
Sequence details1. UNP RESIDUES 71 GLN IS MISSING ACCORDING TO REF.1 OF DATABASE UNIPROTKB/SWISS-PROT P50735 (GUDB_ ...1. UNP RESIDUES 71 GLN IS MISSING ACCORDING TO REF.1 OF DATABASE UNIPROTKB/SWISS-PROT P50735 (GUDB_BACSU). 2. UNP RESIDUES 94-96 (UNP RESIDUES 97-99 ARE REPEAT OF 94-96) ARE MISSING IN SPONTANEOUS MUTANT GUDB1 ACCORDING TO THE DATABASE GUDB_BACSU.

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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: 2.28 Å3/Da / Density % sol: 46.07 % / Mosaicity: 0 °
Crystal growTemperature: 290 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 20% Peg 3350, 0.15M sodium malonate, pH 7, VAPOR DIFFUSION, HANGING DROP, temperature 290K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I02 / Wavelength: 0.97 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Dec 4, 2008
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97 Å / Relative weight: 1
ReflectionResolution: 2.4→19.943 Å / Num. all: 98133 / Num. obs: 96102 / % possible obs: 97.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.6 % / Rsym value: 0.07
Reflection shellResolution: 2.4→2.48 Å / % possible all: 97.8

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
SCALA3.3.15data scaling
MOLREPphasing
PHENIX1.5_2refinement
PDB_EXTRACT3.005data extraction
ADSCQuantumdata collection
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.4→19.769 Å / Occupancy max: 1 / Occupancy min: 1 / FOM work R set: 0.778 / SU ML: 0.41 / σ(F): 1.37 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.278 4788 4.98 %thin resolution shells
Rwork0.247 ---
all0.249 96058 --
obs0.249 96058 97.89 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 31.366 Å2 / ksol: 0.337 e/Å3
Displacement parametersBiso max: 110.48 Å2 / Biso mean: 45.359 Å2 / Biso min: 12.77 Å2
Baniso -1Baniso -2Baniso -3
1-1.906 Å2-0 Å2-2.651 Å2
2---9.613 Å20 Å2
3---7.707 Å2
Refinement stepCycle: LAST / Resolution: 2.4→19.769 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms18294 0 0 497 18791
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00318634
X-RAY DIFFRACTIONf_angle_d0.8225154
X-RAY DIFFRACTIONf_chiral_restr0.0612784
X-RAY DIFFRACTIONf_plane_restr0.0033254
X-RAY DIFFRACTIONf_dihedral_angle_d18.66914
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDTypeRms dev position (Å)
11C3169X-RAY DIFFRACTIONPOSITIONAL0.007
12D3169X-RAY DIFFRACTIONPOSITIONAL0.007
21A2928X-RAY DIFFRACTIONPOSITIONAL0.014
22B2928X-RAY DIFFRACTIONPOSITIONAL0.014
23E2929X-RAY DIFFRACTIONPOSITIONAL0.013
24F2928X-RAY DIFFRACTIONPOSITIONAL0.029
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 30

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.4-2.4270.3291460.2873080322699
2.427-2.4560.3171450.293096324199
2.456-2.4860.3671460.2953100324699
2.486-2.5170.3391640.2933063322799
2.517-2.550.3181760.2993070324699
2.55-2.5850.3491460.2973074322099
2.585-2.6220.3681420.2993110325299
2.622-2.6610.3451760.2983034321099
2.661-2.7020.3491640.2963092325699
2.702-2.7470.3271740.2843016319099
2.747-2.7940.331620.2873116327899
2.794-2.8440.3071710.283036320799
2.844-2.8990.3071760.2933038321499
2.899-2.9580.3081530.2893083323699
2.958-3.0220.2941590.2883037319699
3.022-3.0920.3281530.2763061321498
3.092-3.1690.2891580.2723095325398
3.169-3.2540.3191580.2643018317698
3.254-3.350.2581590.2673005316497
3.35-3.4570.2711660.2513010317697
3.457-3.580.2761650.2483012317796
3.58-3.7230.2721600.2293014317497
3.723-3.8910.2531590.2292970312997
3.891-4.0940.2671540.2262999315396
4.094-4.3480.251520.2082967311996
4.348-4.680.2281580.1992999315796
4.68-5.1430.2451590.2142970312996
5.143-5.870.2531710.2172990316197
5.87-7.3330.2291550.2113061321697
7.333-19.7690.1891610.1873054321597

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