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- PDB-24mp: Crystal structure of the GH134 mannanase from Aspergillus nidulans -

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Basic information

Entry
Database: PDB / ID: 24mp
TitleCrystal structure of the GH134 mannanase from Aspergillus nidulans
ComponentsAnGH134
KeywordsCARBOHYDRATE / GH134 / mannanase
Function / homology: / Glycosyl hydrolase family 134 / extracellular region / ETHANOL / N-PROPANOL / Uncharacterized protein
Function and homology information
Biological speciesAspergillus nidulans FGSC A4 (mold)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.75 Å
AuthorsChen, S.C. / Hsu, C.H.
Funding support Taiwan, 1items
OrganizationGrant numberCountry
National Science Council (NSC, Taiwan)114-2113-M-002-009-MY3 Taiwan
CitationJournal: J.Agric.Food Chem. / Year: 2026
Title: Structural Characterization and Engineering of a GH134 beta-Mannanase from Aspergillus nidulans for Enhancement of Activity and Stability.
Authors: Chen, S.C. / Kuo, P.C. / Chen, W.M. / Sheu, S.Y. / Huang, Y.B. / Huang, C.Y. / Chien, I.W. / Lee, T.H. / Hsu, C.H.
History
DepositionMar 11, 2026Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Sep 23, 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: AnGH134
B: AnGH134
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,5228
Polymers38,2322
Non-polymers2906
Water6,197344
1
A: AnGH134
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,3466
Polymers19,1161
Non-polymers2305
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: AnGH134
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,1762
Polymers19,1161
Non-polymers601
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)115.857, 50.249, 67.667
Angle α, β, γ (deg.)90.000, 105.469, 90.000
Int Tables number5
Space group name H-MC121
Space group name HallC2y
Symmetry operation#1: x,y,z
#2: -x,y,-z
#3: x+1/2,y+1/2,z
#4: -x+1/2,y+1/2,-z
Components on special symmetry positions
IDModelComponents
11A-463-

HOH

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Components

#1: Protein AnGH134


Mass: 19115.895 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Aspergillus nidulans FGSC A4 (mold) / Gene: ANIA_02710 / Production host: Escherichia coli (E. coli) / References: UniProt: Q5B9S0
#2: Chemical
ChemComp-EOH / ETHANOL


Mass: 46.068 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C2H6O
#3: Chemical ChemComp-POL / N-PROPANOL / 1-PROPONOL


Mass: 60.095 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 344 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN
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: 2.48 Å3/Da / Density % sol: 50.46 %
Crystal growTemperature: 283 K / Method: vapor diffusion, sitting drop
Details: 8 mM 1,6-hexanediol, 8 mM 1-butanol, 8 mM 1,2-propanediol, 8 mM 2-propanol, 8 mM 1,4-butanediol, 8 mM 1,3-propanediol, 40 mM imidazole-MES monohydrate (pH 6.1), 9.6% (v/v) precipitant mix (6. ...Details: 8 mM 1,6-hexanediol, 8 mM 1-butanol, 8 mM 1,2-propanediol, 8 mM 2-propanol, 8 mM 1,4-butanediol, 8 mM 1,3-propanediol, 40 mM imidazole-MES monohydrate (pH 6.1), 9.6% (v/v) precipitant mix (6.4% ethylene glycol, 3.2% (w/v) PEG 8000), and 3.0% (w/v) 1,5-diaminopentane dihydrochloride.

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: NSRRC / Beamline: TPS 05A / Wavelength: 0.9998 Å
DetectorType: DECTRIS EIGER2 S 9M / Detector: PIXEL / Date: Oct 30, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9998 Å / Relative weight: 1
ReflectionResolution: 1.75→30 Å / Num. obs: 37139 / % possible obs: 97.9 % / Redundancy: 3.7 % / Biso Wilson estimate: 19.4 Å2 / Rpim(I) all: 0.05 / Net I/σ(I): 14.7
Reflection shellResolution: 1.75→1.81 Å / Num. unique obs: 3258 / CC1/2: 0.809

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Processing

Software
NameVersionClassification
PHENIX1.17.1_3660refinement
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5JTS

5jts


Resolution: 1.75→28.06 Å / SU ML: 0.1642 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 18.0387
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.1866 2000 5.39 %
Rwork0.1597 35137 -
obs0.1612 37137 97.93 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 24.49 Å2
Refinement stepCycle: LAST / Resolution: 1.75→28.06 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2592 0 19 344 2955
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00562661
X-RAY DIFFRACTIONf_angle_d0.70463606
X-RAY DIFFRACTIONf_chiral_restr0.043373
X-RAY DIFFRACTIONf_plane_restr0.004476
X-RAY DIFFRACTIONf_dihedral_angle_d14.1559371
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.75-1.80.28221250.23332191X-RAY DIFFRACTION85.87
1.8-1.840.2081310.21072308X-RAY DIFFRACTION91.83
1.84-1.90.23371400.18812456X-RAY DIFFRACTION96.54
1.9-1.960.23241460.17782559X-RAY DIFFRACTION99.89
1.96-2.030.22471440.17122529X-RAY DIFFRACTION99.96
2.03-2.110.1981460.1592568X-RAY DIFFRACTION99.89
2.11-2.210.19031440.15612534X-RAY DIFFRACTION99.85
2.21-2.320.18331450.1572548X-RAY DIFFRACTION99.74
2.32-2.470.19751450.15612550X-RAY DIFFRACTION99.89
2.47-2.660.22321460.15542564X-RAY DIFFRACTION99.85
2.66-2.930.17171450.15292552X-RAY DIFFRACTION99.7
2.93-3.350.1921480.15232590X-RAY DIFFRACTION99.71
3.35-4.220.15421460.13932560X-RAY DIFFRACTION98.76
4.22-28.060.161490.16652628X-RAY DIFFRACTION99.28
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)
12.91919091648-1.21832440388-1.014922499983.51699420738-1.124989931331.460099423310.009011727523940.167074235999-0.1079536614820.0470707157126-0.0887300753738-0.04978781398960.05498787745410.2292299446680.01927781007410.125884171723-0.00533113283842-0.02170117990260.207001637925-0.06898630853740.158082688097-14.281348770124.6043456879-0.973633260758
22.742846542090.0115776486663-0.8514028276592.357320977831.089181667352.52433278623-0.157706871676-0.218164766479-0.06867362727220.3927077361670.1146871877620.1471800490130.2594655175420.06243261752070.03779044433180.1789302863170.03648560435680.02868089609580.122499694295-0.003640726641120.147109700497-29.970094267323.59133979578.53112666564
33.244307951370.218414630161-0.777792193191.86341375704-0.653702358942.83285822735-0.0807228549301-0.5420072937-0.125724093260.3858890281720.030913625452-0.1515209619920.03556600433480.552350845180.05898758100220.2144126475450.0702342887197-0.04587311050440.275313424044-0.03886716249220.164810419411-13.863108863128.03082107613.5398211667
45.26409670608-1.429677232411.533537738615.61924810302-0.5213851543084.233314463490.294540987925-0.242710315079-0.2906987383580.228856864181-0.243920790743-0.02625713056680.1847856808150.301668423898-0.06850061088140.126162372416-0.0301609818235-0.02559046815030.288857651473-0.01723713800880.201766467539-7.716127832126.3272113176-0.566385908321
53.671762142750.71237661087-4.827134702133.80210611592-0.3935369625736.69151898390.0262808736915-0.3391134298130.503753005554-0.0780665034734-0.0834502708327-0.10689830296-0.1269693441490.602631550976-0.2020723450620.1351776929560.0050143993868-0.04026884703250.2334279853770.006062150964410.226319657368-13.189737274352.363264203533.0448779756
67.754956299666.172059771036.404170709237.960580697186.841460591456.527690993390.171129786671-0.9502351570740.1245020841260.547723859098-0.329161130310.2832041313710.0960036921165-0.2621244988090.1226476223570.128816885902-0.0005765628345530.01807790250930.2227426918060.01771885912640.145365412544-28.168391671544.069116616940.4661695962
74.01771885827-1.881318481190.4653834624374.9915929177-2.417029534442.393798374760.0655435824812-0.0102923849847-0.150283149201-0.119422299844-0.136889947124-0.1446872322740.05881517458070.127631876070.03112573838620.09578685560640.00897295254863-0.003563944489420.132073769061-0.02815998010570.0821342858391-25.757055807743.948562321130.6885660923
84.62946446807-2.273388941181.977271749662.75698380727-2.965735698553.27134631603-0.260172550457-0.401599477610.3448949900320.6374341072480.269761330395-0.304149302938-0.3273248145020.1045198878330.003449879816060.1744716755730.0257944661781-0.02998790623970.190707730855-0.07455033422320.189709345496-29.091870408155.496973985634.1704325573
91.07987555761-0.3207526122390.4446876975133.05735365404-0.1435160640692.203609728160.01471919690750.0317671757937-0.0352212138949-0.07007272871790.05715235167770.1074039932850.0158933226087-0.111939214483-0.09037412989840.0762043774155-0.01011944257030.007669691299150.140479886027-0.01037971262450.121752187908-39.19091828148.576524801524.3948832906
101.45667984941-0.3940710661722.690747448651.89771808381-3.059453736187.99274455152-0.006467175507310.1311603811490.0242128711874-0.120549742692-0.0784614061106-0.1507197666970.1126400727010.2259159871750.08641787660920.08862832787880.02598135176270.02313432132470.135832040287-0.04052612162160.129541982153-22.677259474146.004517053219.2974935851
117.088360243812.78007255203-3.682330794623.681949439720.5526648759723.703068862570.06846292056190.1154038141060.186960804259-0.006699442273280.16794018076-0.0306680902209-0.01530993577760.0345319361832-0.1594551077460.06707279310110.0312156749521-0.04813472015280.195780914294-0.01024801113720.153467768637-16.404067089247.258861393633.4109046274
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 7 through 52 )
2X-RAY DIFFRACTION2chain 'A' and (resid 53 through 116 )
3X-RAY DIFFRACTION3chain 'A' and (resid 117 through 155 )
4X-RAY DIFFRACTION4chain 'A' and (resid 156 through 173 )
5X-RAY DIFFRACTION5chain 'B' and (resid 9 through 19 )
6X-RAY DIFFRACTION6chain 'B' and (resid 20 through 29 )
7X-RAY DIFFRACTION7chain 'B' and (resid 30 through 43 )
8X-RAY DIFFRACTION8chain 'B' and (resid 44 through 52 )
9X-RAY DIFFRACTION9chain 'B' and (resid 53 through 116 )
10X-RAY DIFFRACTION10chain 'B' and (resid 117 through 155 )
11X-RAY DIFFRACTION11chain 'B' and (resid 156 through 173 )

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