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- PDB-8er5: Crystal Structure of NlpC/P60 domain from Clostridium innocuum Nl... -

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Basic information

Entry
Database: PDB / ID: 8er5
TitleCrystal Structure of NlpC/P60 domain from Clostridium innocuum NlpC/P60 domain-containing protein CI_01448.
ComponentsNlpC/P60 domain-containing protein
KeywordsHYDROLASE / NlpC/P60 domain / peptidoglycan hydrolase / CSGID / Structural Genomics / Center for Structural Genomics of Infectious Diseases
Function / homology
Function and homology information


: / NlpC/P60 family / NlpC/P60 domain profile. / Endopeptidase, NLPC/P60 domain / Choline-binding repeat / Putative cell wall binding repeat / Cell wall/choline-binding repeat / Cell wall-binding repeat profile. / Papain-like cysteine peptidase superfamily
Similarity search - Domain/homology
NlpC/P60 domain-containing protein
Similarity search - Component
Biological species[Clostridium] innocuum 2959 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.92 Å
AuthorsMinasov, G. / Shuvalova, L. / Dubrovska, I. / Wiersum, G. / Satchell, K.J.F. / Center for Structural Genomics of Infectious Diseases (CSGID)
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID) United States
CitationJournal: To Be Published
Title: Crystal Structure of NlpC/P60 domain from Clostridium innocuum NlpC/P60 domain-containing protein CI_01448.
Authors: Minasov, G. / Shuvalova, L. / Dubrovska, I. / Wiersum, G. / Satchell, K.J.F.
History
DepositionOct 11, 2022Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 18, 2023Provider: repository / Type: Initial release
Revision 1.1Nov 15, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond / Item: _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_2
Revision 1.2Nov 6, 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

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Assembly

Deposited unit
A: NlpC/P60 domain-containing protein
B: NlpC/P60 domain-containing protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,17714
Polymers25,0622
Non-polymers1,11512
Water5,044280
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2410 Å2
ΔGint-111 kcal/mol
Surface area10770 Å2
MethodPISA
Unit cell
Length a, b, c (Å)51.954, 51.954, 157.440
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number152
Space group name H-MP3121
Components on special symmetry positions
IDModelComponents
11A-713-

HOH

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Components

#1: Protein NlpC/P60 domain-containing protein


Mass: 12531.203 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) [Clostridium] innocuum 2959 (bacteria) / Gene: HMPREF1094_01267 / Plasmid: pMCSG53 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21 / Variant (production host): (DE3)Magic / References: UniProt: N9VDX5
#2: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 280 / 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: 2.45 Å3/Da / Density % sol: 49.74 %
Crystal growTemperature: 292 K / Method: vapor diffusion, sitting drop / pH: 5.6
Details: Protein: 10.0 mg/ml, 0.25M Sodium chloride, 0.01M Tris pH 8.3; Screen: AmSO4 (G4), 1.0M Ammonium sulfate, 0.1M HEPES sodium salt pH 5.6, 2% (w/v) PEG 400; Cryo: 2M Lithium sulfate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-F / Wavelength: 0.97872 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Nov 18, 2020 / Details: BE
RadiationMonochromator: C(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97872 Å / Relative weight: 1
ReflectionResolution: 1.92→30 Å / Num. obs: 19632 / % possible obs: 99.9 % / Observed criterion σ(I): -3 / Redundancy: 6.5 % / Biso Wilson estimate: 21.5 Å2 / CC1/2: 0.988 / CC star: 0.997 / Rmerge(I) obs: 0.137 / Rpim(I) all: 0.058 / Rrim(I) all: 0.149 / Rsym value: 0.137 / Χ2: 1.202 / Net I/σ(I): 15.2
Reflection shellResolution: 1.92→1.95 Å / Redundancy: 6.5 % / Rmerge(I) obs: 0.856 / Mean I/σ(I) obs: 2.6 / Num. unique obs: 959 / CC1/2: 0.779 / CC star: 0.936 / Rpim(I) all: 0.357 / Rrim(I) all: 0.928 / Rsym value: 0.856 / Χ2: 1.008 / % possible all: 99.8

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Processing

Software
NameVersionClassification
REFMAC5.8.0267refinement
PDB_EXTRACT3.27data extraction
HKL-3000data reduction
HKL-3000data scaling
HKL-3000phasing
RefinementMethod to determine structure: SAD / Resolution: 1.92→29.62 Å / Cor.coef. Fo:Fc: 0.966 / Cor.coef. Fo:Fc free: 0.944 / SU B: 5.874 / SU ML: 0.088 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.139 / ESU R Free: 0.134 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.203 995 5.1 %RANDOM
Rwork0.1561 ---
obs0.1584 18593 99.89 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 61.84 Å2 / Biso mean: 22.028 Å2 / Biso min: 14.37 Å2
Baniso -1Baniso -2Baniso -3
1-0.37 Å20.18 Å20 Å2
2--0.37 Å20 Å2
3----1.19 Å2
Refinement stepCycle: final / Resolution: 1.92→29.62 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1734 0 60 291 2085
Biso mean--47.28 33.98 -
Num. residues----251
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0050.0131852
X-RAY DIFFRACTIONr_bond_other_d0.0010.0181597
X-RAY DIFFRACTIONr_angle_refined_deg1.3111.6212536
X-RAY DIFFRACTIONr_angle_other_deg0.3381.5643682
X-RAY DIFFRACTIONr_dihedral_angle_1_deg3.9465257
X-RAY DIFFRACTIONr_dihedral_angle_2_deg30.97222.38163
X-RAY DIFFRACTIONr_dihedral_angle_3_deg8.20815207
X-RAY DIFFRACTIONr_dihedral_angle_4_deg10.612156
X-RAY DIFFRACTIONr_chiral_restr0.0590.2241
X-RAY DIFFRACTIONr_gen_planes_refined0.0550.022205
X-RAY DIFFRACTIONr_gen_planes_other0.050.02423
LS refinement shellResolution: 1.921→1.971 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.218 64 -
Rwork0.21 1353 -
all-1417 -
obs--99.86 %
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)
12.3034-1.0204-0.33770.60290.24351.7719-0.1291-0.09980.2626-0.09220.0033-0.119-0.05120.31960.12580.15960.0653-0.00050.14840.02760.08629.77980.675213.726
20.52850.3622-0.71661.5698-0.34522.4275-0.10930.0241-0.02580.00170.0430.0830.2150.07870.06630.09680.06910.0150.08210.01190.06159.8694-4.86598.3772
33.1437-1.1796-0.57571.94980.0774.3978-0.0556-0.03590.16930.078-0.0969-0.0951-0.23560.35980.15250.03410.0104-0.0090.10140.01530.060219.9784.836217.0437
43.2678-2.07740.56346.00410.67050.8497-0.14020.1116-0.18860.17950.00220.08580.20320.18040.1380.10070.07090.06520.11780.03520.087417.2511-5.921316.9281
52.62662.85310.33283.25790.74931.7069-0.0162-0.2015-0.02590.0893-0.14830.05130.17220.10580.16450.10140.07290.0340.06730.02010.06318.5189-5.293822.5156
62.8880.7915-1.65062.5174-1.57264.6712-0.009-0.2713-0.1790.0192-0.229-0.13620.11180.63220.23790.04250.05660.00130.13620.04250.065319.4782-4.149121.8639
79.8062.3492.94380.68480.45292.0675-0.09920.35-0.3159-0.04220.1166-0.04150.0212-0.0159-0.01740.05510.02610.00590.0578-0.01750.0682-9.52191.98774.5003
81.4621-0.78080.31216.1140.47862.21790.0132-0.0906-0.0393-0.0693-0.0735-0.0603-0.16920.04550.06020.06460.04320.00770.06530.00340.0484-0.91416.691716.6134
91.0322-0.6293-0.28653.22412.0584.92510.05340.09520.0486-0.01710.0371-0.0723-0.18750.1775-0.09050.04490.025-0.00630.0401-0.0030.037-0.488215.65710.8717
103.16170.9732-0.14090.6026-0.93582.854-0.08340.1839-0.0396-0.0060.05570.0044-0.084-0.19530.02780.08950.05850.00320.1766-0.04740.1125-11.604110.84856.1348
112.0450.74260.40.6420.7272.23340.01320.0382-0.05440.0716-0.06380.0223-0.1221-0.09870.05060.10590.0521-0.00890.1144-0.00570.1062-10.414214.657417.352
121.7059-0.8592-1.14361.24080.6734.805-0.02020.1976-0.08870.0586-0.10980.0608-0.1052-0.48440.130.01240.0147-0.00520.0672-0.01030.0422-17.212512.13615.1135
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A289 - 315
2X-RAY DIFFRACTION2A316 - 348
3X-RAY DIFFRACTION3A349 - 363
4X-RAY DIFFRACTION4A364 - 375
5X-RAY DIFFRACTION5A376 - 397
6X-RAY DIFFRACTION6A398 - 414
7X-RAY DIFFRACTION7B290 - 301
8X-RAY DIFFRACTION8B302 - 318
9X-RAY DIFFRACTION9B319 - 337
10X-RAY DIFFRACTION10B338 - 365
11X-RAY DIFFRACTION11B366 - 393
12X-RAY DIFFRACTION12B394 - 414

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