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- PDB-9lp6: Crystal structure of phenolic acid decarboxylase Mav Pad (Mycobac... -

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Basic information

Entry
Database: PDB / ID: 9lp6
TitleCrystal structure of phenolic acid decarboxylase Mav Pad (Mycobacterium avium)
ComponentsPhenolic acid decarboxylase
KeywordsOXIDOREDUCTASE / Phenolic acid decarboxylase
Function / homologyPhenolic acid decarboxylase / Phenolic acid decarboxylase (PAD) / carboxy-lyase activity / Calycin / Phenolic acid decarboxylase
Function and homology information
Biological speciesMycobacterium avium (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.91 Å
AuthorsWu, B. / Yu, L. / Wang, Y.H.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: To Be Published
Title: Crystal structure of phenolic acid decarboxylase Mav Pad (Mycobacterium avium)
Authors: Wu, B. / Yu, L. / Wang, Y.H.
History
DepositionJan 24, 2025Deposition site: PDBJ / Processing site: PDBC
Revision 1.0Jan 28, 2026Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Phenolic acid decarboxylase
B: Phenolic acid decarboxylase
C: Phenolic acid decarboxylase


Theoretical massNumber of molelcules
Total (without water)55,6313
Polymers55,6313
Non-polymers00
Water8,737485
1
A: Phenolic acid decarboxylase
B: Phenolic acid decarboxylase


Theoretical massNumber of molelcules
Total (without water)37,0872
Polymers37,0872
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2610 Å2
ΔGint-15 kcal/mol
Surface area12680 Å2
MethodPISA
2
C: Phenolic acid decarboxylase

C: Phenolic acid decarboxylase


Theoretical massNumber of molelcules
Total (without water)37,0872
Polymers37,0872
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation10_664-y+1,-x+1,-z-1/61
Buried area2580 Å2
ΔGint-16 kcal/mol
Surface area12810 Å2
MethodPISA
Unit cell
Length a, b, c (Å)66.373, 66.373, 474.856
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number178
Space group name H-MP6122
Space group name HallP612(x,y,z+5/12)
Components on special symmetry positions
IDModelComponents
11B-332-

HOH

21C-252-

HOH

31C-284-

HOH

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Components

#1: Protein Phenolic acid decarboxylase


Mass: 18543.650 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium avium (bacteria) / Gene: CKJ66_03625 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A2A2ZQM8
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 485 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationN

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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: 2.71 Å3/Da / Density % sol: 54.68 %
Crystal growTemperature: 289.15 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 1.6M Ammonium sulfate 0.1M MES momohydrate pH 6.5 10% v/v 1,4-Dioxane

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL18U1 / Wavelength: 0.987 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Sep 14, 2024
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.987 Å / Relative weight: 1
ReflectionResolution: 1.91→57.47 Å / Num. obs: 50601 / % possible obs: 99.9 % / Redundancy: 18.6 % / CC1/2: 0.977 / Net I/σ(I): 7.2
Reflection shellResolution: 1.91→2.01 Å / Num. unique obs: 50601 / CC1/2: 0.61

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Processing

Software
NameVersionClassification
PHENIX1.19.2_4158refinement
autoPROCdata reduction
autoPROCdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.91→55.87 Å / SU ML: 0.2483 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 22.6976
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2673 1995 3.96 %
Rwork0.227 48340 -
obs0.2285 50335 99.83 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 26.29 Å2
Refinement stepCycle: LAST / Resolution: 1.91→55.87 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3756 0 0 485 4241
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00763876
X-RAY DIFFRACTIONf_angle_d0.97685288
X-RAY DIFFRACTIONf_chiral_restr0.0662546
X-RAY DIFFRACTIONf_plane_restr0.0096689
X-RAY DIFFRACTIONf_dihedral_angle_d6.5585518
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.91-1.950.34781400.30743395X-RAY DIFFRACTION100
1.95-2.010.37281360.28233306X-RAY DIFFRACTION99.31
2.01-2.060.32121410.28083374X-RAY DIFFRACTION100
2.06-2.130.28871390.25773368X-RAY DIFFRACTION100
2.13-2.210.26481400.24353398X-RAY DIFFRACTION100
2.21-2.30.28511400.23843387X-RAY DIFFRACTION100
2.3-2.40.25711400.2343388X-RAY DIFFRACTION100
2.4-2.530.30411400.23983404X-RAY DIFFRACTION100
2.53-2.690.29321420.24573432X-RAY DIFFRACTION100
2.69-2.890.31361450.24093476X-RAY DIFFRACTION100
2.89-3.180.2681420.22393471X-RAY DIFFRACTION100
3.18-3.640.25181460.20263509X-RAY DIFFRACTION99.97
3.64-4.590.21111480.18193588X-RAY DIFFRACTION99.92
4.59-5.870.24021560.22193844X-RAY DIFFRACTION98.62
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)
12.21281918461-0.5607391395140.6079028344031.470578525250.02615971867133.069982362170.0839412626956-0.280458996590.0847941361592-0.05928621847090.004384760654530.219294710382-0.00479455048001-0.0826649511882-0.0456730802110.183300728391-0.0334472418370.01720292439840.142288074527-0.07223202242260.176244057311-33.998782516931.4383159964-13.5455423838
21.73051049011-0.687226543716-0.2164330605331.921583896090.1543727353941.5336309136-0.0485475306903-0.2081228081590.08616737234770.0750438772080.09549146959940.002378793381930.04553383632250.0389661271518-0.02170806871030.134879813842-0.0112882424967-0.00933896019660.160983006668-0.06758152758070.14280791677-29.360794931327.0732421982-10.2727193934
33.09605820745-1.436642295110.01096561310911.93795364122-0.1900658244522.63041934382-0.175923356734-0.05125784484780.372868971238-0.05829257441830.132030796908-0.110756923731-0.1462222832850.1786177189970.03368037125130.205291025923-0.00684278457387-0.05263497830660.17431410431-0.09195732831640.192064971167-18.734719528411.4714554953-25.9866173832
40.7536860448610.1437670828820.09104132368861.823162795251.215714999752.08203544584-0.00981484634460.00424764026889-0.07886074413520.0307372054960.128689845657-0.2225663907830.08090092077160.301858218475-0.09784908797740.149928802110.014665149875-0.01628088392150.231386368195-0.07342199690970.170817570361-14.006995439814.6991400339-19.6808420355
51.773427576352.158451478530.7978574667224.264872452641.957335103034.294772947470.0607211279692-0.0855737938041-0.379336799416-0.400762028455-0.138947931734-0.7389803701030.662875617198-0.169315790257-0.1277179842450.5022402856970.0213404325182-0.1603173195470.254360999109-0.01032309148020.33555207560811.506656685720.7568001425-30.2132871265
62.01407044606-0.52366895584-0.09029907596272.78138242121-0.7021819523152.20506117669-0.0264813996552-0.3425727581410.02947087270460.1574336458010.116707646522-0.09345353683340.0194358010612-0.277679957465-0.1032338661840.118517967571-0.00658255206733-0.02298224530340.214889338886-0.007803059232090.1690082504039.8931810022537.0854288015-24.1503767872
72.609382442810.891950604064-0.02757382383242.625161807840.8197067234853.870539952530.158111881548-0.1499806718220.009903046012870.137539445898-0.0514744409367-0.2450070137670.0467619194815-0.469142273517-0.02645217336250.1726722509840.0115903153389-0.03926020916940.249292048973-0.007494323949310.175655516196.3833772908734.8878856062-27.4801669763
81.68265952260.669808849429-0.003455145067762.24787797840.1105956430912.85753944880.128751223828-0.2659457837030.11815071690.0911443530173-0.1833944952370.123800126107-0.502256739899-0.617531718828-0.02650943798960.2096969991950.0636885897018-0.01909773643420.336708067595-0.04529200480730.1498497508063.6707649394940.5601436447-30.8834242958
90.335439535243-0.2178963303610.1990414001190.332513247478-0.5672003643751.08895718249-0.0736529684662-0.4777238961560.140366567410.3105780680690.1680358933910.110322424058-0.421306109364-0.695788112719-0.07823449788370.5265770546820.468939548669-0.03515170125790.936218918869-0.03445946379630.405842809341-9.7918760580246.0434082075-31.6421426721
101.343597515990.07960095500510.2683844165341.63084932263-0.2157989120162.96516524266-0.00708413832549-0.3060917013070.0343537887830.2056764044570.001790914677110.097056295872-0.194770545045-0.4530071268160.02496956454990.224647949928-0.0121397748243-0.03243745282270.251956591517-0.03382513285670.19378997622610.96768941936.0986219198-23.2819754734
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION

IDRefine TLS-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11chain 'A' and (resid 1 through 52 )AA1 - 521 - 52
22chain 'A' and (resid 53 through 152 )AA53 - 15253 - 152
33chain 'B' and (resid 1 through 60 )BB1 - 601 - 60
44chain 'B' and (resid 61 through 152 )BB61 - 15261 - 152
55chain 'C' and (resid 1 through 10 )CC1 - 101 - 10
66chain 'C' and (resid 11 through 37 )CC11 - 3711 - 37
77chain 'C' and (resid 38 through 60 )CC38 - 6038 - 60
88chain 'C' and (resid 61 through 109 )CC61 - 10961 - 109
99chain 'C' and (resid 110 through 125 )CC110 - 125110 - 125
1010chain 'C' and (resid 126 through 152 )CC126 - 152126 - 152

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