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- PDB-9kk9: Structure of the transaminase PhnW from Vibrio vulnificus in comp... -

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Basic information

Entry
Database: PDB / ID: 9kk9
TitleStructure of the transaminase PhnW from Vibrio vulnificus in complex with PLP and AEP
Components2-aminoethylphosphonate--pyruvate transaminase
KeywordsTRANSFERASE / transaminase/aminotransferase / 2-aminoethylphosphonate (AEP) / pyridoxal phosphate (PLP) / Vibrio vulnificus
Function / homology(2-aminoethyl)phosphonic acid
Function and homology information
Biological speciesVibrio vulnificus NBRC 15645 = ATCC 27562 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.15 Å
AuthorsMa, Q. / Han, M.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC) China
CitationJournal: To Be Published
Title: Structure of the transaminase PhnW from Vibrio vulnificus in complex with PLP and AEP
Authors: Ma, Q. / Han, M.
History
DepositionNov 13, 2024Deposition site: PDBJ / Processing site: PDBC
Revision 1.0Nov 19, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: 2-aminoethylphosphonate--pyruvate transaminase
B: 2-aminoethylphosphonate--pyruvate transaminase
C: 2-aminoethylphosphonate--pyruvate transaminase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)122,5116
Polymers122,1363
Non-polymers3753
Water5,675315
1
A: 2-aminoethylphosphonate--pyruvate transaminase
B: 2-aminoethylphosphonate--pyruvate transaminase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)81,6744
Polymers81,4242
Non-polymers2502
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5430 Å2
ΔGint-27 kcal/mol
Surface area23970 Å2
MethodPISA
2
C: 2-aminoethylphosphonate--pyruvate transaminase
hetero molecules

C: 2-aminoethylphosphonate--pyruvate transaminase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)81,6744
Polymers81,4242
Non-polymers2502
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_556-x,y,-z+11
Buried area5450 Å2
ΔGint-25 kcal/mol
Surface area23950 Å2
MethodPISA
Unit cell
Length a, b, c (Å)158.248, 94.945, 91.184
Angle α, β, γ (deg.)90.00, 90.51, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11C-583-

HOH

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Components

#1: Protein 2-aminoethylphosphonate--pyruvate transaminase


Mass: 40712.098 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Details: Sequence reference for strain 'NBRC 15645 = ATCC 27562' is not available in UniProt at the time of biocuration. The author provided reference sequence from NCBI (id: WP_026050740.1).
Source: (gene. exp.) Vibrio vulnificus NBRC 15645 = ATCC 27562 (bacteria)
Gene: phnW, VVA0476 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: 2-aminoethylphosphonate-pyruvate transaminase
#2: Chemical ChemComp-P7I / (2-aminoethyl)phosphonic acid


Mass: 125.064 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C2H8NO3P / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 315 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
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: 2.82 Å3/Da / Density % sol: 56.38 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: The complex crystals were grown in drops containing 1.5 ul of protein solution (25 mg/ml protein in 10 mM HEPES pH 7.5, 150 mM NaCl, 1 mM DTT, 50 mM AEP and 2.3 mM PLP) and 1.5 ul of ...Details: The complex crystals were grown in drops containing 1.5 ul of protein solution (25 mg/ml protein in 10 mM HEPES pH 7.5, 150 mM NaCl, 1 mM DTT, 50 mM AEP and 2.3 mM PLP) and 1.5 ul of reservoir solution (100 mM Bis-Tris pH5.9, 25% (w/v) PEG3350)

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.9792 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jul 14, 2024
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 2.15→60.87 Å / Num. obs: 72999 / % possible obs: 99.4 % / Redundancy: 6.5 % / CC1/2: 0.994 / Rpim(I) all: 0.045 / Rrim(I) all: 0.113 / Rsym value: 0.104 / Net I/σ(I): 9.7
Reflection shellResolution: 2.15→2.157 Å / Mean I/σ(I) obs: 2 / Num. unique obs: 700 / CC1/2: 0.893 / Rpim(I) all: 0.287 / Rrim(I) all: 0.757 / Rsym value: 0.7 / % possible all: 97.4

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Processing

Software
NameVersionClassification
BUSTER2.10.2refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.15→60.87 Å / Cor.coef. Fo:Fc: 0.95 / Cor.coef. Fo:Fc free: 0.938 / SU R Cruickshank DPI: 0.173 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.169 / SU Rfree Blow DPI: 0.138 / SU Rfree Cruickshank DPI: 0.141
RfactorNum. reflection% reflectionSelection details
Rfree0.189 3532 4.84 %RANDOM
Rwork0.167 ---
obs0.168 72970 99.4 %-
Displacement parametersBiso mean: 50.18 Å2
Baniso -1Baniso -2Baniso -3
1--3.0824 Å20 Å2-1.1325 Å2
2---9.815 Å20 Å2
3---12.8974 Å2
Refine analyzeLuzzati coordinate error obs: 0.24 Å
Refinement stepCycle: 1 / Resolution: 2.15→60.87 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8391 0 66 315 8772
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.018649HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.0611739HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d2940SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes201HARMONIC2
X-RAY DIFFRACTIONt_gen_planes1278HARMONIC5
X-RAY DIFFRACTIONt_it8649HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_omega_torsion3.52
X-RAY DIFFRACTIONt_other_torsion17.43
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion1149SEMIHARMONIC5
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_contact11002SEMIHARMONIC4
LS refinement shellResolution: 2.15→2.21 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.247 247 4.61 %
Rwork0.202 5114 -
all0.204 5361 -
obs--99.15 %
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)
11.154-0.4336-0.30861.7970.77021.31-0.0901-0.3011-0.00270.17470.14960.07070.0856-0.0134-0.0594-0.14950.07760.0050.04820.0418-0.1586-42.498573.660830.0443
21.4289-0.6138-0.35911.62160.64231.00740.09160.1924-0.0811-0.46470.00630.0531-0.1585-0.1056-0.0980.01210.0066-0.0325-0.07450.0113-0.1707-38.083167.4085-0.333
31.66720.09350.88610.64610.01051.46470.09370.3020.1294-0.1405-0.08870.02250.07620.1443-0.005-0.10690.05450.05360.01480.0271-0.1353-4.451547.420430.4757
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1{ A|* }
2X-RAY DIFFRACTION2{ B|* }
3X-RAY DIFFRACTION3{ C|* }

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