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- PDB-6uuk: Crystal structure of muramoyltetrapeptide carboxypeptidase from O... -

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Basic information

Entry
Database: PDB / ID: 6uuk
TitleCrystal structure of muramoyltetrapeptide carboxypeptidase from Oxalobacter formigenes
ComponentsMuramoyltetrapeptide carboxypeptidase
KeywordsHYDROLASE / LD-carboxy peptidase / Structural Genomics / Midwest Center for Structural Genomics / MCSG / PSI-Biology
Function / homology
Function and homology information


muramoyltetrapeptide carboxypeptidase / muramoyltetrapeptide carboxypeptidase activity / serine-type peptidase activity / proteolysis
Similarity search - Function
Peptidase family S66 / LD-carboxypeptidase A, C-terminal domain superfamily / Murein tetrapeptide carboxypeptidase, N-terminal / LD-carboxypeptidase, N-terminal / LD-carboxypeptidase, C-terminal / LD-carboxypeptidase N-terminal domain / LD-carboxypeptidase C-terminal domain / Class I glutamine amidotransferase-like
Similarity search - Domain/homology
Muramoyltetrapeptide carboxypeptidase
Similarity search - Component
Biological speciesOxalobacter formigenes OXCC13 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.348 Å
AuthorsChang, C. / Tesar, C. / Endres, M. / Babnigg, G. / Hassan, H. / Joachimiak, A. / Midwest Center for Structural Genomics (MCSG)
CitationJournal: To Be Published
Title: Crystal structure of muramoyltetrapeptide carboxypeptidase from Oxalobacter formigenes
Authors: Chang, C. / Tesar, C. / Endres, M. / Babnigg, G. / Hassan, H. / Joachimiak, A. / Midwest Center for Structural Genomics (MCSG)
History
DepositionOct 30, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 4, 2020Provider: repository / Type: Initial release
Revision 1.1Oct 11, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.2Nov 15, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond / Item: _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_2
Revision 1.3Oct 23, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Muramoyltetrapeptide carboxypeptidase
B: Muramoyltetrapeptide carboxypeptidase


Theoretical massNumber of molelcules
Total (without water)78,8302
Polymers78,8302
Non-polymers00
Water41423
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3530 Å2
ΔGint-8 kcal/mol
Surface area21510 Å2
MethodPISA
Unit cell
Length a, b, c (Å)82.443, 82.443, 149.293
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number173
Space group name H-MP63

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Components

#1: Protein Muramoyltetrapeptide carboxypeptidase


Mass: 39414.793 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Oxalobacter formigenes OXCC13 (bacteria)
Gene: idcA, OFBG_01115 / Production host: Escherichia coli BL21(DE3) (bacteria)
References: UniProt: C3XA61, muramoyltetrapeptide carboxypeptidase
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 23 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN
Has protein modificationY

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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: 1.86 Å3/Da / Density % sol: 33.8 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 7.5 / Details: 0.1 M HEPES, 25% PEG3350, 0.2M sodium chloride

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.97918 Å
DetectorType: DECTRIS PILATUS3 X 6M / Detector: PIXEL / Date: Jul 6, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97918 Å / Relative weight: 1
Reflection twinOperator: h,-h-k,-l / Fraction: 0.5
ReflectionResolution: 2.348→50 Å / Num. obs: 23955 / % possible obs: 99.9 % / Redundancy: 6.5 % / Rmerge(I) obs: 0.099 / Rpim(I) all: 0.04 / Rrim(I) all: 0.107 / Χ2: 0.834 / Net I/σ(I): 6.5
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
2.348-2.394.40.7611560.5050.3790.8540.94199.1
2.39-2.435.20.71412220.5120.3260.7890.95599.8
2.43-2.485.80.60511760.6480.2640.6630.89899.9
2.48-2.536.10.54311750.6780.230.5920.919100
2.53-2.596.30.50412270.8180.2110.5490.92599.8
2.59-2.656.10.43311930.8260.1850.4730.893100
2.65-2.716.40.36411760.9020.1510.3950.93100
2.71-2.7970.35511980.880.140.3830.89499.9
2.79-2.8770.26512130.9240.1050.2860.846100
2.87-2.966.90.22411730.9510.0890.2420.84299.9
2.96-3.076.80.18712100.9540.0760.2030.852100
3.07-3.196.70.15411940.9730.0630.1670.832100
3.19-3.336.30.10811980.9820.0450.1180.8199.9
3.33-3.517.10.09611860.9880.0380.1040.83599.9
3.51-3.737.10.07412120.9880.0290.080.7699.8
3.73-4.026.90.06511910.9910.0260.070.72599.9
4.02-4.426.40.05612020.9930.0240.0610.705100
4.42-5.067.20.05312120.9960.0210.0570.685100
5.06-6.376.70.05412160.9920.0220.0590.68899.9
6.37-506.80.05412250.9950.0210.0580.87299.4

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Processing

Software
NameVersionClassification
SCALEPACKdata scaling
PHENIX1.14_3260refinement
PDB_EXTRACT3.25data extraction
HKL-3000data reduction
HKL-3000phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1zrs

1zrs


Resolution: 2.348→40.826 Å / Cross valid method: THROUGHOUT / σ(F): 144.59 / Phase error: 25.12
RfactorNum. reflection% reflection
Rfree0.2293 1209 5.38 %
Rwork0.2039 --
obs0.2093 22968 95.82 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 100.79 Å2 / Biso mean: 28.3973 Å2 / Biso min: 8.38 Å2
Refinement stepCycle: final / Resolution: 2.348→40.826 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4451 0 0 23 4474
Biso mean---22.81 -
Num. residues----574
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 9

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.348-2.44450.38271080.26111734184266
2.4445-2.55570.32731330.24972375250890
2.5557-2.69030.32121180.24452508262695
2.6903-2.85870.22131400.23962521266195
2.8587-3.07910.25691230.24082529265295
3.0791-3.38850.24371640.22062483264794
3.3885-3.87770.24181350.20372521265695
3.8777-4.8810.17911470.15822521266894
4.881-27.54860.21141410.18872546268795

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