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- PDB-4kna: Crystal structure of an N-succinylglutamate 5-semialdehyde dehydr... -

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Basic information

Entry
Database: PDB / ID: 4kna
TitleCrystal structure of an N-succinylglutamate 5-semialdehyde dehydrogenase from Burkholderia thailandensis
ComponentsN-succinylglutamate 5-semialdehyde dehydrogenase
KeywordsOXIDOREDUCTASE / NIAID / National Institute of Allergy and Infectious Diseases / Seattle Structural Genomics Center for Infectious Disease / SSGCID / structural genomics / NAD-dependent / N-succinyl-L-glutamate / amido acid degradation / AST pathway / aldehyde dehydrogenase
Function / homology
Function and homology information


succinylglutamate-semialdehyde dehydrogenase / succinylglutamate-semialdehyde dehydrogenase activity / arginine catabolic process to succinate / arginine catabolic process to glutamate
Similarity search - Function
Succinylglutamate-semialdehyde dehydrogenase / Aldehyde Dehydrogenase; Chain A, domain 2 / Aldehyde Dehydrogenase; Chain A, domain 2 / Aldehyde Dehydrogenase; Chain A, domain 1 / Aldehyde Dehydrogenase; Chain A, domain 1 / Aldehyde dehydrogenase, glutamic acid active site / Aldehyde dehydrogenases glutamic acid active site. / Aldehyde dehydrogenase, cysteine active site / Aldehyde dehydrogenases cysteine active site. / Aldehyde dehydrogenase domain ...Succinylglutamate-semialdehyde dehydrogenase / Aldehyde Dehydrogenase; Chain A, domain 2 / Aldehyde Dehydrogenase; Chain A, domain 2 / Aldehyde Dehydrogenase; Chain A, domain 1 / Aldehyde Dehydrogenase; Chain A, domain 1 / Aldehyde dehydrogenase, glutamic acid active site / Aldehyde dehydrogenases glutamic acid active site. / Aldehyde dehydrogenase, cysteine active site / Aldehyde dehydrogenases cysteine active site. / Aldehyde dehydrogenase domain / Aldehyde dehydrogenase family / Aldehyde dehydrogenase, N-terminal / Aldehyde dehydrogenase, C-terminal / Aldehyde/histidinol dehydrogenase / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
N-succinylglutamate 5-semialdehyde dehydrogenase
Similarity search - Component
Biological speciesBurkholderia thailandensis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.95 Å
AuthorsSeattle Structural Genomics Center for Infectious Disease (SSGCID)
CitationJournal: TO BE PUBLISHED
Title: Crystal structure of an N-succinylglutamate 5-semialdehyde dehydrogenase from Burkholderia thailandensis
Authors: Edwards, T.E. / Abendroth, J. / Seattle Structural Genomics Center for Infectious Disease (SSGCID)
History
DepositionMay 9, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 5, 2013Provider: repository / Type: Initial release
Revision 1.1Feb 28, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / 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_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.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_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: N-succinylglutamate 5-semialdehyde dehydrogenase
B: N-succinylglutamate 5-semialdehyde dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)106,02510
Polymers105,6252
Non-polymers3998
Water15,601866
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9060 Å2
ΔGint-74 kcal/mol
Surface area32510 Å2
MethodPISA
Unit cell
Length a, b, c (Å)170.050, 120.690, 53.910
Angle α, β, γ (deg.)90.000, 107.360, 90.000
Int Tables number5
Space group name H-MC121

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Components

#1: Protein N-succinylglutamate 5-semialdehyde dehydrogenase / AstD / Succinylglutamic semialdehyde dehydrogenase / SGSD


Mass: 52812.672 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Burkholderia thailandensis (bacteria) / Strain: E264 / ATCC 700388 / DSM 13276 / CIP 106301 / Gene: astD, BTH_I1778 / Plasmid: pBG1861 / Production host: Escherichia coli (E. coli)
References: UniProt: Q2SXN9, succinylglutamate-semialdehyde dehydrogenase
#2: Chemical ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#3: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C2H6O2
#4: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ca
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 866 / 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: 2.5 Å3/Da / Density % sol: 50.79 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: 31 mg/mL ButhA.00020.d.B1.PS01757 against Morpheus screen condition A10: 10% PEG8000, 20% ethylene glycol, 0.03 M magnesium chloride, 0.03 M calcium chloride, 0.1 M bicine/Trizma, pH 8.5, ...Details: 31 mg/mL ButhA.00020.d.B1.PS01757 against Morpheus screen condition A10: 10% PEG8000, 20% ethylene glycol, 0.03 M magnesium chloride, 0.03 M calcium chloride, 0.1 M bicine/Trizma, pH 8.5, crystal tracking ID 243761a10, unique puck ID pna1-4, VAPOR DIFFUSION, SITTING DROP, temperature 289K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-D / Wavelength: 1.07811 Å
DetectorType: RAYONIX MX-300 / Detector: CCD / Date: Apr 11, 2013
RadiationMonochromator: Kohzu Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.07811 Å / Relative weight: 1
ReflectionResolution: 1.95→50 Å / Num. all: 75602 / Num. obs: 75481 / % possible obs: 99.8 % / Observed criterion σ(I): -3 / Redundancy: 6.3 % / Biso Wilson estimate: 32.62 Å2 / Rmerge(I) obs: 0.09 / Net I/σ(I): 13.09
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. unique obs% possible all
1.95-26.30.5143.4435413559099.8
2-2.060.4154.2434251539699.9
2.06-2.120.3315.3334385263100
2.12-2.180.2676.4832887516499.7
2.18-2.250.2227.64316044969100
2.25-2.330.1948.7130604481499.7
2.33-2.420.1699.78295864632100
2.42-2.520.14111.628225443499.8
2.52-2.630.12712.9127343429699.8
2.63-2.760.11114.6825947410199.9
2.76-2.910.09417.0224683391499.8
2.91-3.080.08518.8123017368499.7
3.08-3.30.07720.64214633467100
3.3-3.560.0722.4119857323899.8
3.56-3.90.06523.89181412977100
3.9-4.360.06324.6116440270399.5
4.36-5.030.0625.5414562237699.9
5.03-6.170.06125.312571202499.6
6.17-8.720.05625.889813157599.7
8.72-500.05325.63511886498.4

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Phasing

PhasingMethod: molecular replacement
Phasing MRModel details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation3 Å49.21 Å
Translation3 Å49.21 Å

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Processing

Software
NameVersionClassificationNB
XSCALEdata scaling
PHASER2.5.2phasing
REFMACrefinement
PDB_EXTRACT3.11data extraction
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.95→49.26 Å / Cor.coef. Fo:Fc: 0.966 / Cor.coef. Fo:Fc free: 0.952 / WRfactor Rfree: 0.2011 / WRfactor Rwork: 0.1592 / Occupancy max: 1 / Occupancy min: 0.3 / FOM work R set: 0.8954 / SU B: 5.552 / SU ML: 0.085 / SU R Cruickshank DPI: 0.1383 / SU Rfree: 0.1286 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.138 / ESU R Free: 0.129 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: U VALUES : WITH TLS ADDED HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.1921 3800 5 %RANDOM
Rwork0.1524 ---
obs0.1544 75480 99.97 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 72.52 Å2 / Biso mean: 29.1039 Å2 / Biso min: 13.08 Å2
Baniso -1Baniso -2Baniso -3
1--0.09 Å2-0 Å2-1.04 Å2
2---1.12 Å2-0 Å2
3---1.29 Å2
Refinement stepCycle: LAST / Resolution: 1.95→49.26 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7230 0 20 866 8116
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0197462
X-RAY DIFFRACTIONr_bond_other_d0.0010.027069
X-RAY DIFFRACTIONr_angle_refined_deg1.4461.94410178
X-RAY DIFFRACTIONr_angle_other_deg0.801316150
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.8085991
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.40422.766329
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.959151079
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.3911571
X-RAY DIFFRACTIONr_chiral_restr0.0850.21140
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0218746
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021777
X-RAY DIFFRACTIONr_mcbond_it1.1251.8563910
X-RAY DIFFRACTIONr_mcbond_other1.1251.8563909
X-RAY DIFFRACTIONr_mcangle_it1.6692.7784889
LS refinement shellResolution: 1.95→2.001 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.233 285 -
Rwork0.194 5295 -
all-5580 -
obs--100 %
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)
10.50780.35160.31360.56650.49960.7583-0.12070.08620.0775-0.14910.05650.1141-0.1404-0.00670.06420.0579-0.0158-0.01150.0370.03020.054233.710225.3387-19.4323
20.52830.25880.4530.5670.19920.70610.01050.0821-0.06410.07680.0594-0.13730.00430.051-0.070.02680.00590.00350.0287-0.01190.067157.892617.54983.6663
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 487
2X-RAY DIFFRACTION2B2 - 487

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