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- PDB-6w7x: Crystal structure of N-acetylornithine aminotransferase from Sten... -

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Basic information

Entry
Database: PDB / ID: 6w7x
TitleCrystal structure of N-acetylornithine aminotransferase from Stenotrophomonas maltophilia K279a
ComponentsAcetylornithine aminotransferase
KeywordsTRANSFERASE / SSGCID / Stenotrophomonas maltophilia / N-acetylornithine aminotransferase / argD / Structural Genomics / Seattle Structural Genomics Center for Infectious Disease
Function / homology
Function and homology information


acetylornithine transaminase / N2-acetyl-L-ornithine:2-oxoglutarate 5-aminotransferase activity / arginine biosynthetic process / pyridoxal phosphate binding / cytoplasm
Similarity search - Function
Acetylornithine/Succinylornithine transaminase family / Aminotransferases class-III pyridoxal-phosphate attachment site. / Aminotransferase class-III / Aminotransferase class-III / Aspartate Aminotransferase, domain 1 / Aspartate Aminotransferase, domain 1 / Aspartate Aminotransferase; domain 2 / Type I PLP-dependent aspartate aminotransferase-like (Major domain) / Pyridoxal phosphate-dependent transferase, small domain / Pyridoxal phosphate-dependent transferase, major domain ...Acetylornithine/Succinylornithine transaminase family / Aminotransferases class-III pyridoxal-phosphate attachment site. / Aminotransferase class-III / Aminotransferase class-III / Aspartate Aminotransferase, domain 1 / Aspartate Aminotransferase, domain 1 / Aspartate Aminotransferase; domain 2 / Type I PLP-dependent aspartate aminotransferase-like (Major domain) / Pyridoxal phosphate-dependent transferase, small domain / Pyridoxal phosphate-dependent transferase, major domain / Pyridoxal phosphate-dependent transferase / Alpha-Beta Complex / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Acetylornithine aminotransferase
Similarity search - Component
Biological speciesStenotrophomonas maltophilia (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsSeattle Structural Genomics Center for Infectious Disease (SSGCID)
CitationJournal: To be Published
Title: Crystal structure of N-acetylornithine aminotransferase from Stenotrophomonas maltophilia K279a
Authors: Abendroth, J. / Yano, J.K. / Horanyi, P.S. / Lorimer, D.D. / Edwards, T.E.
History
DepositionMar 19, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 15, 2020Provider: repository / Type: Initial release
Revision 1.1Oct 18, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Acetylornithine aminotransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)44,7102
Polymers44,6181
Non-polymers921
Water2,702150
1
A: Acetylornithine aminotransferase
hetero molecules

A: Acetylornithine aminotransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)89,4204
Polymers89,2362
Non-polymers1842
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation5_554x-y,-y,-z-1/31
Buried area5790 Å2
ΔGint-45 kcal/mol
Surface area25550 Å2
MethodPISA
Unit cell
Length a, b, c (Å)63.820, 63.820, 172.480
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number152
Space group name H-MP3121
Space group name HallP312"
Symmetry operation#1: x,y,z
#2: -y,x-y,z+1/3
#3: -x+y,-x,z+2/3
#4: x-y,-y,-z+2/3
#5: -x,-x+y,-z+1/3
#6: y,x,-z

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Components

#1: Protein Acetylornithine aminotransferase / ACOAT


Mass: 44617.930 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Stenotrophomonas maltophilia (strain K279a) (bacteria)
Strain: K279a / Gene: astC, argD, Smlt3876 / Plasmid: StmaA.01026.b.B1 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: B2FT38, acetylornithine transaminase
#2: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 150 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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 %
Crystal growTemperature: 290 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 29.8 mg/mL StmaA.01026.b.B1.PW38742 against Molecular Dimensions Morpheus screen, condition a7 (10% w/V PEG4000, 20% V/V glycerol, 30 mM magnesium chloride, 30 mM calcium chloride, 100 mM ...Details: 29.8 mg/mL StmaA.01026.b.B1.PW38742 against Molecular Dimensions Morpheus screen, condition a7 (10% w/V PEG4000, 20% V/V glycerol, 30 mM magnesium chloride, 30 mM calcium chloride, 100 mM MOPS/HEPES sodium, pH 7.5), direct cryoprotection, tray 313920a7, puck mnd6-1

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-F / Wavelength: 0.97872 Å
DetectorType: RAYONIX MX-300 / Detector: CCD / Date: Mar 12, 2020
RadiationMonochromator: diamond(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97872 Å / Relative weight: 1
ReflectionResolution: 1.9→50 Å / Num. obs: 33007 / % possible obs: 99.8 % / Redundancy: 7.265 % / Biso Wilson estimate: 44.929 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.064 / Rrim(I) all: 0.068 / Χ2: 1.05 / Net I/σ(I): 15.7
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique obsCC1/2Rrim(I) all% possible all
1.9-1.955.5050.6472.3324030.9210.71499.9
1.95-26.8890.4663.623450.9630.50399.9
2-2.067.6910.3694.822880.9740.395100
2.06-2.127.6950.2916.322000.9790.311100
2.12-2.197.7610.2138.3821420.9910.22799.9
2.19-2.277.6850.1769.8520810.9920.188100
2.27-2.367.6570.1412.0820290.9950.15100
2.36-2.457.6250.11814.3619220.9950.12699.7
2.45-2.567.6260.10616.0718650.9960.11499.9
2.56-2.697.580.08918.4817820.9970.09599.9
2.69-2.837.4920.07721.2716940.9980.08399.9
2.83-37.4140.06824.0316050.9970.07399.8
3-3.217.2930.0632615360.9980.06799.9
3.21-3.477.1250.0628.2514280.9970.06499.8
3.47-3.87.0630.05629.4213220.9980.0699.9
3.8-4.257.0080.05330.2712120.9970.05799.7
4.25-4.917.1110.04930.9710620.9980.05399.6
4.91-6.017.0920.04730.79200.9980.051100
6.01-8.56.7980.04630.277410.9980.0599.6
8.5-505.660.04827.694300.9950.05393.3

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Processing

Software
NameVersionClassification
XDSdata reduction
XSCALEdata scaling
PHENIX1.17.1refinement
PDB_EXTRACT3.25data extraction
MR-Rosettaphasing
PHASERphasing
Cootmodel building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 4JEV

4jev


Resolution: 1.9→46.53 Å / SU ML: 0.1962 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 24.4731 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2127 1850 5.62 %0
Rwork0.1822 ---
obs0.1839 32897 99.64 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 54.28 Å2
Refinement stepCycle: LAST / Resolution: 1.9→46.53 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2666 0 6 150 2822
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00522734
X-RAY DIFFRACTIONf_angle_d0.75873704
X-RAY DIFFRACTIONf_chiral_restr0.0476420
X-RAY DIFFRACTIONf_plane_restr0.0043492
X-RAY DIFFRACTIONf_dihedral_angle_d21.0819975
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.9-1.950.32841160.27812360X-RAY DIFFRACTION99.44
1.95-2.010.27571360.23972353X-RAY DIFFRACTION99.32
2.01-2.070.25931530.22192312X-RAY DIFFRACTION99.56
2.07-2.150.26051480.20332337X-RAY DIFFRACTION99.88
2.15-2.230.2481070.19832397X-RAY DIFFRACTION99.72
2.23-2.340.23131530.19922360X-RAY DIFFRACTION99.88
2.34-2.460.25791760.19322357X-RAY DIFFRACTION99.72
2.46-2.610.29361210.2072371X-RAY DIFFRACTION100
2.61-2.810.23181530.21022373X-RAY DIFFRACTION99.8
2.81-3.10.23561490.1992387X-RAY DIFFRACTION99.76
3.1-3.540.2361580.18982427X-RAY DIFFRACTION99.85
3.55-4.470.17931290.15462454X-RAY DIFFRACTION99.77
4.47-46.530.1631510.15992559X-RAY DIFFRACTION98.8
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)
12.94964612590.3317448819121.284054415223.05919926359-2.535259507272.92085530417-0.05344174524510.105691009532-0.448093184705-1.002184337460.1170244708870.04553728506740.400600122411-0.600334939323-0.05832990029060.642961703774-0.2460909533350.02291238344710.625373209236-0.01053728845840.347092552889-2.80603704933-17.7585016125-26.7502177251
23.945224875722.16901382101-0.6848501508585.94468551408-2.853479610353.855032928710.0710216349708-0.1183542878580.2874907354660.2016269449270.001225403755610.374198104242-0.328931910265-0.576946653545-0.003521675523670.496542742680.1453444785780.02408708531770.64391105083-0.05622201291060.305176204684-4.107242741618.06035829-26.3178081785
32.727297650490.2768155568291.094266253271.979229513730.4545580679233.70067146699-0.0416848755202-0.07268404047060.2789302568970.364438678124-0.242814923612-0.264345858761-0.990362781752-0.2305108495920.2385475774240.64992901135-0.0413130096987-0.0606400964570.3035544455820.05061760740110.30420123661913.22500724216.87992972104-16.6466544243
43.71636406041.2826365041-0.3793900836455.79538280251-0.9803150502112.73852886118-0.0585125058308-0.00928603318008-0.336913520165-0.287123240387-0.0334218805239-0.6708017282050.09658248736580.5081872560440.01737633066180.565966424135-0.206934259179-0.1202389488280.3878639525860.03065113911840.62085618963329.8757117181-5.51832022612-13.0126832696
53.251658642850.5883934553250.8361047850631.94120150988-0.2061159653712.741935057780.121941898673-0.275284266604-0.2277998120590.476316855651-0.186461284291-0.473503886488-0.282630942316-0.2480298780780.00260865796280.587476070557-0.204918016212-0.1415475507350.350539683810.07713856653170.36489402524118.8673661384-4.74301867632-7.09793191604
64.08304113598-1.128516680611.553414146321.870092113680.7065074413024.66515752808-0.140219921509-0.09195636946320.2286087377190.134199308508-0.02673644242990.0165360049689-0.773684677308-0.5412770762570.1462031439360.5654387530960.0278423897285-0.02247053804030.409748925161-0.01213502046260.2482467273785.473296205123.13533228308-16.794381598
70.9887252582740.7939775983890.6434509565714.49578535225-0.3407695365942.335462710050.310091090076-0.293893383565-0.4432114748760.595761326499-0.147596422373-0.33450368980.552125784334-0.740597872961-0.08047920728820.620239811628-0.384154058261-0.07394968391870.5346950997030.1069139519590.4420618104614.21081187197-25.8323003665-12.016887852
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 8 through 58 )
2X-RAY DIFFRACTION2chain 'A' and (resid 59 through 81 )
3X-RAY DIFFRACTION3chain 'A' and (resid 82 through 124 )
4X-RAY DIFFRACTION4chain 'A' and (resid 125 through 183 )
5X-RAY DIFFRACTION5chain 'A' and (resid 184 through 250 )
6X-RAY DIFFRACTION6chain 'A' and (resid 251 through 305 )
7X-RAY DIFFRACTION7chain 'A' and (resid 306 through 416 )

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