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- PDB-8vrm: Crystal structure of the Pcryo_0619 N-acetyltransferase from Psyc... -

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Basic information

Entry
Database: PDB / ID: 8vrm
TitleCrystal structure of the Pcryo_0619 N-acetyltransferase from Psychrobacter cryohalolentis K5
ComponentsAcetyltransferase, putative
KeywordsTRANSFERASE / psychrobacter / N-acetyltransferase / 2 / 3 / 4-triacetoamido-2 / 4-trideoxy-l-arabinose
Function / homology: / Hexapeptide repeat of succinyl-transferase / Hexapeptide transferase, conserved site / Hexapeptide-repeat containing-transferases signature. / Hexapeptide repeat / Bacterial transferase hexapeptide (six repeats) / acyltransferase activity / Trimeric LpxA-like superfamily / Acetyltransferase, putative
Function and homology information
Biological speciesPsychrobacter cryohalolentis K5 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.75 Å
AuthorsDunsirn, M.M. / Bockhaus, N.J. / Thoden, J.B. / Holden, H.M.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R35 GM134643 United States
CitationJournal: To Be Published
Title: Biochemical Investigation of the Enzymes Required for the Production of 2,3,4-triacetoamido-2,3,4-trideoxy-l-arabinose in Psychrobacter cryohalolentis K5
Authors: Bockhaus, N.J. / Dunsirn, M.M. / Thoden, J.B. / Holden, H.M.
History
DepositionJan 22, 2024Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 31, 2024Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Acetyltransferase, putative
B: Acetyltransferase, putative
C: Acetyltransferase, putative
D: Acetyltransferase, putative
E: Acetyltransferase, putative
F: Acetyltransferase, putative
hetero molecules


Theoretical massNumber of molelcules
Total (without water)122,60758
Polymers117,5916
Non-polymers5,01652
Water7,458414
1
A: Acetyltransferase, putative
B: Acetyltransferase, putative
C: Acetyltransferase, putative
hetero molecules


Theoretical massNumber of molelcules
Total (without water)61,66633
Polymers58,7963
Non-polymers2,87030
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area14900 Å2
ΔGint-408 kcal/mol
Surface area20310 Å2
MethodPISA
2
D: Acetyltransferase, putative
E: Acetyltransferase, putative
F: Acetyltransferase, putative
hetero molecules


Theoretical massNumber of molelcules
Total (without water)60,94125
Polymers58,7963
Non-polymers2,14622
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area15200 Å2
ΔGint-388 kcal/mol
Surface area20390 Å2
MethodPISA
Unit cell
Length a, b, c (Å)106.670, 106.670, 180.400
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number173
Space group name H-MP63

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Components

#1: Protein
Acetyltransferase, putative


Mass: 19598.547 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Psychrobacter cryohalolentis K5 (bacteria)
Gene: Pcryo_0619 / Production host: Escherichia coli (E. coli) / Variant (production host): Rosetta2(DE3) / References: UniProt: Q1QD51
#2: Chemical...
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 46 / Source method: obtained synthetically / Formula: SO4
#3: Chemical
ChemComp-MPD / (4S)-2-METHYL-2,4-PENTANEDIOL


Mass: 118.174 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C6H14O2 / Comment: precipitant*YM
#4: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6O2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 414 / 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: 2.52 Å3/Da / Density % sol: 51.18 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8
Details: 2.2-2.5 M ammonium sulfate, 2% hexyleneglycol, 100 mM HEPPS (pH 8)

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-BM / Wavelength: 0.9792 Å
DetectorType: ADSC QUANTUM 270 / Detector: CCD / Date: Aug 9, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 1.75→50 Å / Num. obs: 114484 / % possible obs: 98.5 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 8 % / Rsym value: 0.066 / Net I/σ(I): 31.5
Reflection shellResolution: 1.75→1.78 Å / Redundancy: 4.5 % / Mean I/σ(I) obs: 1.9 / Num. unique obs: 5577 / Rsym value: 0.44 / % possible all: 95.7

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Processing

Software
NameVersionClassification
REFMAC5.8.0405refinement
HKL-3000data reduction
HKL-3000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.75→46.19 Å / Cor.coef. Fo:Fc: 0.965 / Cor.coef. Fo:Fc free: 0.947 / SU B: 3.28 / SU ML: 0.098 / Cross valid method: THROUGHOUT / ESU R: 0.115 / ESU R Free: 0.117 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.2297 5779 5 %RANDOM
Rwork0.18683 ---
obs0.18893 108704 98.37 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 31.142 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å2-0 Å2
2--0 Å2-0 Å2
3----0.01 Å2
Refinement stepCycle: 1 / Resolution: 1.75→46.19 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8066 0 270 414 8750
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0128423
X-RAY DIFFRACTIONr_bond_other_d0.0010.0168138
X-RAY DIFFRACTIONr_angle_refined_deg1.3421.62911397
X-RAY DIFFRACTIONr_angle_other_deg0.4471.57518782
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.62251063
X-RAY DIFFRACTIONr_dihedral_angle_2_deg8.843536
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.602101476
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.0580.21340
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.029353
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021731
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_it2.5182.8774267
X-RAY DIFFRACTIONr_mcbond_other2.5172.8774267
X-RAY DIFFRACTIONr_mcangle_it3.3945.1555325
X-RAY DIFFRACTIONr_mcangle_other3.3945.1565326
X-RAY DIFFRACTIONr_scbond_it4.3933.5924156
X-RAY DIFFRACTIONr_scbond_other4.3923.5924157
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other6.5156.3346073
X-RAY DIFFRACTIONr_long_range_B_refined8.04229.29337
X-RAY DIFFRACTIONr_long_range_B_other8.04229.29338
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.752→1.797 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.338 411 -
Rwork0.358 7782 -
obs--95.41 %

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