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- PDB-9np9: Crystal structure of the inactive conformation of a glycoside hyd... -

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Basic information

Entry
Database: PDB / ID: 9np9
TitleCrystal structure of the inactive conformation of a glycoside hydrolase (CapGH2b - E553Q Mutant) from the GH2 family in the space group I213 at 2.6 A
ComponentsGlycoside hydrolase family 2
KeywordsHYDROLASE / Redox-regulation / glycosyl hydrolase / mannosidase / redox-switch / metagenome / disulfide bond
Function / homologyPHOSPHATE ION
Function and homology information
Biological speciesmetagenome (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.6 Å
AuthorsMartins, M.P. / Spadeto, J.P.M. / Miyamoto, R.Y. / Morais, M.A.B. / Murakami, M.T.
Funding support Brazil, 3items
OrganizationGrant numberCountry
Sao Paulo Research Foundation (FAPESP)2021/04891-3 Brazil
Sao Paulo Research Foundation (FAPESP)2021/09793-0 Brazil
Sao Paulo Research Foundation (FAPESP)2022/06298-0 Brazil
CitationJournal: To Be Published
Title: Crystal structure of the inactive conformation of a glycoside hydrolase (CapGH2b - E553Q Mutant) from the GH2 family in the space group I213 at 2.6 A
Authors: Martins, M.P. / Spadeto, J.P.M. / Miyamoto, R.Y. / Morais, M.A.B. / Murakami, M.T.
History
DepositionMar 11, 2025Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 12, 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: Glycoside hydrolase family 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)91,0063
Polymers90,8161
Non-polymers1902
Water2,936163
1
A: Glycoside hydrolase family 2
hetero molecules

A: Glycoside hydrolase family 2
hetero molecules

A: Glycoside hydrolase family 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)273,0179
Polymers272,4473
Non-polymers5706
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation8_555-z,x+1/2,-y+1/21
crystal symmetry operation11_455y-1/2,-z+1/2,-x1
Buried area9080 Å2
ΔGint-71 kcal/mol
Surface area79970 Å2
MethodPISA
Unit cell
Length a, b, c (Å)190.913, 190.913, 190.913
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number199
Space group name H-MI213

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Components

#1: Protein Glycoside hydrolase family 2


Mass: 90815.602 Da / Num. of mol.: 1 / Mutation: E553Q
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) metagenome (others) / Production host: Escherichia coli BL21(DE3) (bacteria) / References: beta-mannosidase
#2: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: PO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 163 / 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: 3.19 Å3/Da / Density % sol: 61.47 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop
Details: 1 M ammonium phosphate dibasic, 0.1 M sodium acetate, pH 4.5, 0.1 M praseodyminium

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: LNLS SIRIUS / Beamline: MANACA / Wavelength: 1.36999 Å
DetectorType: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Oct 9, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.36999 Å / Relative weight: 1
ReflectionResolution: 2.6→47.73 Å / Num. obs: 35630 / % possible obs: 99.5 % / Redundancy: 40.9 % / CC1/2: 0.977 / Rmerge(I) obs: 0.281 / Rrim(I) all: 0.318 / Net I/σ(I): 4.74
Reflection shell
Resolution (Å)Rmerge(I) obsNum. unique obsCC1/2Rrim(I) allDiffraction-ID
2.6-2.762.76756080.093.1181
2.76-2.951.71753570.2611.9381
2.95-3.180.98249950.5311.1111
3.18-3.480.49245580.8270.561
3.48-3.890.25742060.9410.291
3.89-4.490.15936870.9780.1791
4.49-5.490.1331550.9830.1471
5.49-7.710.12524720.9850.1421
7.71-47.730.06614280.9950.0741

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Processing

Software
NameVersionClassification
PHENIX(1.20.1_4487: ???)refinement
XDSdata scaling
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.6→47.73 Å / SU ML: 0.33 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 26.06 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2346 1779 5 %
Rwork0.1975 --
obs0.1993 35591 99.89 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.6→47.73 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5850 0 10 163 6023
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0026010
X-RAY DIFFRACTIONf_angle_d0.5088162
X-RAY DIFFRACTIONf_dihedral_angle_d15.3312190
X-RAY DIFFRACTIONf_chiral_restr0.043861
X-RAY DIFFRACTIONf_plane_restr0.0041061
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.6-2.670.31771330.32752548X-RAY DIFFRACTION99
2.67-2.750.32271360.3022593X-RAY DIFFRACTION100
2.75-2.840.33851350.29152553X-RAY DIFFRACTION100
2.84-2.940.31041370.28922605X-RAY DIFFRACTION100
2.94-3.060.3271360.2842591X-RAY DIFFRACTION100
3.06-3.20.29851350.2522569X-RAY DIFFRACTION100
3.2-3.360.27231370.23432598X-RAY DIFFRACTION100
3.36-3.570.25331360.20522579X-RAY DIFFRACTION100
3.57-3.850.23051370.18952605X-RAY DIFFRACTION100
3.85-4.240.18411380.15972624X-RAY DIFFRACTION100
4.24-4.850.19721380.15062611X-RAY DIFFRACTION100
4.85-6.10.20411380.16972629X-RAY DIFFRACTION100
6.11-47.730.20561430.16952707X-RAY DIFFRACTION100
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)
11.3147-0.33760.1841.0562-0.46121.3981-0.03240.1255-0.0397-0.1910.0334-0.101-0.05520.2259-0.00470.5642-0.03040.06670.5597-0.0490.4668-30.716139.412519.959
21.75610.2343-0.2525.9658-1.04511.7036-0.06340.1562-0.2174-0.26240.13620.28260.1573-0.2603-0.07860.45890.0085-0.06730.4691-0.04070.4581-65.815739.036120.7398
31.35210.4066-0.51732.0183-0.50621.1313-0.1214-0.0397-0.3555-0.17890.0477-0.12420.40890.09720.07140.65090.0178-0.02290.4839-0.0210.548-47.76411.66730.7517
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 23 through 222 )
2X-RAY DIFFRACTION2chain 'A' and (resid 223 through 349 )
3X-RAY DIFFRACTION3chain 'A' and (resid 350 through 796 )

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