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- PDB-9i4z: Thomasclavelia ramosa IgA peptidase active site mutant - E540A -

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Basic information

Entry
Database: PDB / ID: 9i4z
TitleThomasclavelia ramosa IgA peptidase active site mutant - E540A
ComponentsIgA protease
KeywordsHYDROLASE / Protease / Metallopeptidase / Metzincin
Function / homology
Function and homology information


cellulose catabolic process / metallopeptidase activity / proteolysis / extracellular region / membrane
Similarity search - Function
Domain of unknown function DUF6273 / Domain of unknown function (DUF6273) / Peptidase M64, IgA / IgA Peptidase M64 / Carbohydrate binding X2 domain / Carbohydrate binding domain X2 / LPXTG cell wall anchor motif / LPXTG cell wall anchor domain / Metallopeptidase, catalytic domain superfamily / Immunoglobulin E-set / Immunoglobulin-like fold
Similarity search - Domain/homology
FORMIC ACID / IgA protease
Similarity search - Component
Biological speciesThomasclavelia ramosa (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.75 Å
AuthorsRamirez-Larrota, J.S. / Eckhard, U. / Gomis-Ruth, F.X.
Funding support Spain, 3items
OrganizationGrant numberCountry
Agencia Estatal de Investigacion (AEI)PRE2020-096731 Spain
Agencia Estatal de Investigacion (AEI)PID2019-107725RB-I00 Spain
Agencia Estatal de Investigacion (AEI)RYC2020-029773-I Spain
CitationJournal: To Be Published
Title: Thomasclavelia ramosa IgA peptidase active site mutant - E540A
Authors: Ramirez-Larrota, J.S. / Eckhard, U. / Gomis-Ruth, F.X.
History
DepositionJan 27, 2025Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 25, 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: IgA protease
hetero molecules


Theoretical massNumber of molelcules
Total (without water)64,75413
Polymers63,8861
Non-polymers86812
Water7,746430
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2140 Å2
ΔGint-12 kcal/mol
Surface area22690 Å2
Unit cell
Length a, b, c (Å)46.15, 87.83, 67.47
Angle α, β, γ (deg.)90, 96.11, 90
Int Tables number4
Space group name H-MP1211

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Components

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Protein , 1 types, 1 molecules A

#1: Protein IgA protease


Mass: 63885.918 Da / Num. of mol.: 1 / Mutation: E540A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thomasclavelia ramosa (bacteria) / Gene: iga / Plasmid: pCri7b / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q9AES2

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Non-polymers , 5 types, 442 molecules

#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-PG4 / TETRAETHYLENE GLYCOL


Mass: 194.226 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H18O5 / Comment: precipitant*YM
#4: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C2H6O2
#5: Chemical ChemComp-FMT / FORMIC ACID


Mass: 46.025 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: CH2O2
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 430 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY
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: 2.12 Å3/Da / Density % sol: 42.09 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8 / Details: PEG3350, sodium fluoride / PH range: 7-8

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ALBA / Beamline: XALOC / Wavelength: 0.9792 Å
DetectorType: DECTRIS PILATUS3 X 6M / Detector: PIXEL / Date: Apr 19, 2023
Details: KB mirrors (VFM and HFM in Kirkpatrick-Baez configuration)
RadiationMonochromator: Channel-cut Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 1.75→45.9 Å / Num. obs: 53460 / % possible obs: 99.1 % / Redundancy: 6.4 % / CC1/2: 0.99 / Rmerge(I) obs: 0.077 / Rrim(I) all: 0.083 / Net I/σ(I): 13.3
Reflection shellResolution: 1.75→1.86 Å / Redundancy: 4.9 % / Rmerge(I) obs: 1.563 / Mean I/σ(I) obs: 1.23 / Num. unique obs: 8622 / CC1/2: 0.458 / % possible all: 96

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Processing

Software
NameVersionClassification
BUSTER2.10.4refinement
SHELXEmodel building
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.75→45.89 Å / Cor.coef. Fo:Fc: 0.968 / Cor.coef. Fo:Fc free: 0.955 / SU R Cruickshank DPI: 0.119 / Cross valid method: THROUGHOUT / SU R Blow DPI: 0.122 / SU Rfree Blow DPI: 0.114 / SU Rfree Cruickshank DPI: 0.113
RfactorNum. reflection% reflectionSelection details
Rfree0.2133 701 -RANDOM
Rwork0.1779 ---
obs0.1784 53460 99.2 %-
Displacement parametersBiso mean: 36.48 Å2
Baniso -1Baniso -2Baniso -3
1--0.7847 Å20 Å20.03 Å2
2---2.1139 Å20 Å2
3---2.8987 Å2
Refine analyzeLuzzati coordinate error obs: 0.22 Å
Refinement stepCycle: LAST / Resolution: 1.75→45.89 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4409 0 50 430 4889
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.0094583HARMONIC2
X-RAY DIFFRACTIONt_angle_deg0.886198HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d2098SINUSOIDAL2
X-RAY DIFFRACTIONt_gen_planes784HARMONIC5
X-RAY DIFFRACTIONt_it4583HARMONIC10
X-RAY DIFFRACTIONt_chiral_improper_torsion586SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies5HARMONIC1
X-RAY DIFFRACTIONt_utility_distance9HARMONIC1
X-RAY DIFFRACTIONt_ideal_dist_contact4206SEMIHARMONIC4
X-RAY DIFFRACTIONt_omega_torsion3.86
X-RAY DIFFRACTIONt_other_torsion2.55
LS refinement shellResolution: 1.75→1.77 Å
RfactorNum. reflection% reflection
Rfree0.4429 27 -
Rwork0.3605 --
obs0.3619 1528 87.83 %
Refinement TLS params.

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)
10.5138-0.0851-0.12730.4550.12420.5046-0.01660.030.04640.030.03670.04520.04640.0452-0.0201-0.0202-0.0039-0.0123-0.03020.0092-0.001923.72436.77931.1869
20.92890.05890.14440.9083-0.22351.63840.0108-0.144-0.232-0.144-0.06880.1766-0.2320.17660.0580.0076-0.02340.0113-0.00060.0154-0.092434.229246.2032-28.8892
31.88820.0783-1.10350.5851-0.3141.4614-0.0217-0.1261-0.071-0.12610.1053-0.0879-0.071-0.0879-0.0836-0.0223-0.0098-0.0321-0.06760.00470.05339.778957.7376-5.845
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1{A|330 - 632 A|998 - 998 A|999 - 999}A330 - 632
2X-RAY DIFFRACTION1{A|330 - 632 A|998 - 998 A|999 - 999}A998 - 999
3X-RAY DIFFRACTION2{A|633 - 807}A633 - 807
4X-RAY DIFFRACTION3{A|808 - 876 A|901 - 901}A808 - 901

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