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- PDB-8gsm: Crystal Structure of VibMO1 -

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Basic information

Entry
Database: PDB / ID: 8gsm
TitleCrystal Structure of VibMO1
Components4-hydroxybenzoate decarboxylase
KeywordsBIOSYNTHETIC PROTEIN / VibMO1
Function / homology: / FAD-binding domain / FAD binding domain / FAD binding / monooxygenase activity / FAD/NAD(P)-binding domain superfamily / FLAVIN-ADENINE DINUCLEOTIDE / 4-hydroxybenzoate decarboxylase
Function and homology information
Biological speciesBoreostereum vibrans (fungus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.88 Å
AuthorsYing, Z. / Feng, K.N.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC) China
CitationJournal: To Be Published
Title: Crystal Structure of VibMO1
Authors: Ying, Z. / Feng, K.N.
History
DepositionSep 6, 2022Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Sep 13, 2023Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
G: 4-hydroxybenzoate decarboxylase
H: 4-hydroxybenzoate decarboxylase
I: 4-hydroxybenzoate decarboxylase
J: 4-hydroxybenzoate decarboxylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)208,1386
Polymers206,5674
Non-polymers1,5712
Water00
1
G: 4-hydroxybenzoate decarboxylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)52,4272
Polymers51,6421
Non-polymers7861
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
H: 4-hydroxybenzoate decarboxylase


Theoretical massNumber of molelcules
Total (without water)51,6421
Polymers51,6421
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
I: 4-hydroxybenzoate decarboxylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)52,4272
Polymers51,6421
Non-polymers7861
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
J: 4-hydroxybenzoate decarboxylase


Theoretical massNumber of molelcules
Total (without water)51,6421
Polymers51,6421
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)120.430, 127.780, 146.450
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Space group name HallP2ac2ab
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x,y+1/2,-z+1/2
#4: -x+1/2,-y,z+1/2

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Components

#1: Protein
4-hydroxybenzoate decarboxylase


Mass: 51641.758 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Boreostereum vibrans (fungus) / Gene: MO1 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A167KUL3
#2: Chemical ChemComp-FAD / FLAVIN-ADENINE DINUCLEOTIDE


Mass: 785.550 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C27H33N9O15P2 / Comment: FAD*YM
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: 2.73 Å3/Da / Density % sol: 54.9 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / Details: Sodium bromide , PEG 3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL18U1 / Wavelength: 0.9792 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Dec 8, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 2.88→50 Å / Num. obs: 52795 / % possible obs: 99.05 % / Redundancy: 9.3 % / Biso Wilson estimate: 58.8 Å2 / Rmerge(I) obs: 0.175 / Rpim(I) all: 0.094 / Net I/σ(I): 21.15
Reflection shellResolution: 2.88→2.98 Å / Redundancy: 9.8 % / Rmerge(I) obs: 0.768 / Mean I/σ(I) obs: 3.02 / Num. unique obs: 5019 / Rpim(I) all: 0.613 / % possible all: 98

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Processing

Software
NameVersionClassification
PHENIX1.18.1_3865refinement
HKL-3000data reduction
HKL-3000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5EOW

5eow


Resolution: 2.88→48.14 Å / SU ML: 0.5181 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 32.919
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2931 1985 3.87 %
Rwork0.2337 49340 -
obs0.236 51325 99.08 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 61.81 Å2
Refinement stepCycle: LAST / Resolution: 2.88→48.14 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms13825 0 106 0 13931
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.009814287
X-RAY DIFFRACTIONf_angle_d1.169419410
X-RAY DIFFRACTIONf_chiral_restr0.17162100
X-RAY DIFFRACTIONf_plane_restr0.0072514
X-RAY DIFFRACTIONf_dihedral_angle_d22.2935244
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.88-2.950.47991330.41433429X-RAY DIFFRACTION97.78
2.95-3.030.4391410.38043463X-RAY DIFFRACTION98.66
3.03-3.120.40711490.35673445X-RAY DIFFRACTION98.55
3.12-3.220.4041380.32783460X-RAY DIFFRACTION98.82
3.22-3.340.35351350.30883490X-RAY DIFFRACTION98.99
3.34-3.470.34791370.28313506X-RAY DIFFRACTION99.1
3.47-3.630.38191420.24483503X-RAY DIFFRACTION99.4
3.63-3.820.311430.23663482X-RAY DIFFRACTION98.43
3.82-4.060.30361470.22623517X-RAY DIFFRACTION99.65
4.06-4.370.26371340.19013549X-RAY DIFFRACTION99.78
4.37-4.810.23881500.1793556X-RAY DIFFRACTION99.76
4.81-5.510.26921440.18813583X-RAY DIFFRACTION99.6
5.51-6.930.26491420.21693616X-RAY DIFFRACTION99.71
6.94-48.140.18681500.18133741X-RAY DIFFRACTION99.01

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