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- PDB-8xup: Crystal structure of lipoprotein NlpI in complex with MepS -

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Basic information

Entry
Database: PDB / ID: 8xup
TitleCrystal structure of lipoprotein NlpI in complex with MepS
Components
  • Lipoprotein NlpI
  • Murein DD-endopeptidase MepS/Murein LD-carboxypeptidase
KeywordsPROTEIN BINDING / hydrolases / lipoprotein / protease / protein complex
Function / homology
Function and homology information


muramoyltetrapeptide carboxypeptidase activity / muramoyltetrapeptide carboxypeptidase / capsule polysaccharide biosynthetic process / peptidoglycan metabolic process / peptidoglycan turnover / Hydrolases; Acting on peptide bonds (peptidases) / cysteine-type peptidase activity / cell outer membrane / cell wall organization / protein-macromolecule adaptor activity ...muramoyltetrapeptide carboxypeptidase activity / muramoyltetrapeptide carboxypeptidase / capsule polysaccharide biosynthetic process / peptidoglycan metabolic process / peptidoglycan turnover / Hydrolases; Acting on peptide bonds (peptidases) / cysteine-type peptidase activity / cell outer membrane / cell wall organization / protein-macromolecule adaptor activity / endopeptidase activity / receptor-mediated virion attachment to host cell / cell cycle / cell division / protein homodimerization activity / proteolysis / plasma membrane
Similarity search - Function
Lipoprotein NlpI / NlpC/P60 domain profile. / Endopeptidase, NLPC/P60 domain / NlpC/P60 family / Tetratricopeptide repeat / TPR repeat region circular profile. / TPR repeat profile. / Tetratricopeptide repeats / Tetratricopeptide repeat / Papain-like cysteine peptidase superfamily ...Lipoprotein NlpI / NlpC/P60 domain profile. / Endopeptidase, NLPC/P60 domain / NlpC/P60 family / Tetratricopeptide repeat / TPR repeat region circular profile. / TPR repeat profile. / Tetratricopeptide repeats / Tetratricopeptide repeat / Papain-like cysteine peptidase superfamily / Prokaryotic membrane lipoprotein lipid attachment site profile. / Tetratricopeptide-like helical domain superfamily
Similarity search - Domain/homology
Lipoprotein NlpI / Murein DD-endopeptidase MepS/Murein LD-carboxypeptidase
Similarity search - Component
Biological speciesEscherichia coli K-12 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.8 Å
AuthorsTzeng, S.R. / Wang, S. / Huang, C.H.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: To Be Published
Title: Crystal structure of lipoprotein NlpI in complex with MepS
Authors: Tzeng, S.R. / Wang, S. / Huang, C.H. / Lin, T.S.
History
DepositionJan 13, 2024Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jun 5, 2024Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Lipoprotein NlpI
B: Lipoprotein NlpI
C: Lipoprotein NlpI
D: Lipoprotein NlpI
E: Murein DD-endopeptidase MepS/Murein LD-carboxypeptidase
F: Murein DD-endopeptidase MepS/Murein LD-carboxypeptidase
G: Murein DD-endopeptidase MepS/Murein LD-carboxypeptidase
H: Murein DD-endopeptidase MepS/Murein LD-carboxypeptidase
I: Murein DD-endopeptidase MepS/Murein LD-carboxypeptidase
J: Murein DD-endopeptidase MepS/Murein LD-carboxypeptidase
K: Murein DD-endopeptidase MepS/Murein LD-carboxypeptidase
L: Murein DD-endopeptidase MepS/Murein LD-carboxypeptidase


Theoretical massNumber of molelcules
Total (without water)289,51812
Polymers289,51812
Non-polymers00
Water6,197344
1
A: Lipoprotein NlpI
B: Lipoprotein NlpI
E: Murein DD-endopeptidase MepS/Murein LD-carboxypeptidase
G: Murein DD-endopeptidase MepS/Murein LD-carboxypeptidase
I: Murein DD-endopeptidase MepS/Murein LD-carboxypeptidase
J: Murein DD-endopeptidase MepS/Murein LD-carboxypeptidase


Theoretical massNumber of molelcules
Total (without water)144,7596
Polymers144,7596
Non-polymers00
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area13250 Å2
ΔGint-52 kcal/mol
Surface area46730 Å2
MethodPISA
2
C: Lipoprotein NlpI
D: Lipoprotein NlpI
F: Murein DD-endopeptidase MepS/Murein LD-carboxypeptidase
H: Murein DD-endopeptidase MepS/Murein LD-carboxypeptidase
K: Murein DD-endopeptidase MepS/Murein LD-carboxypeptidase
L: Murein DD-endopeptidase MepS/Murein LD-carboxypeptidase


Theoretical massNumber of molelcules
Total (without water)144,7596
Polymers144,7596
Non-polymers00
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area13210 Å2
ΔGint-51 kcal/mol
Surface area46080 Å2
MethodPISA
Unit cell
Length a, b, c (Å)197.193, 99.439, 196.244
Angle α, β, γ (deg.)90.000, 104.450, 90.000
Int Tables number5
Space group name H-MC121

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Components

#1: Protein
Lipoprotein NlpI


Mass: 34082.734 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli K-12 (bacteria) / Gene: nlpI, yhbM, b3163, JW3132 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P0AFB1
#2: Protein
Murein DD-endopeptidase MepS/Murein LD-carboxypeptidase / Lipoprotein Spr / Murein hydrolase MepS


Mass: 19148.357 Da / Num. of mol.: 8
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli K-12 (bacteria) / Gene: mepS, spr, yeiV, b2175, JW2163 / Production host: Escherichia coli BL21(DE3) (bacteria)
References: UniProt: P0AFV4, Hydrolases; Acting on peptide bonds (peptidases), muramoyltetrapeptide carboxypeptidase
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 344 / Source method: isolated from a natural source / Formula: H2O

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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: 3.23 Å3/Da / Density % sol: 61.96 %
Crystal growTemperature: 277.15 K / Method: vapor diffusion, hanging drop
Details: 1.4M sodium acetate, 0.1M sodium cacodylate, pH 6.5

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: NSRRC / Beamline: TPS 05A / Wavelength: 1 Å
DetectorType: RAYONIX MX300-HS / Detector: CCD / Date: Nov 9, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.8→30 Å / Num. obs: 90404 / % possible obs: 99.9 % / Redundancy: 3.8 % / Biso Wilson estimate: 57.02 Å2 / Rmerge(I) obs: 0.073 / Rpim(I) all: 0.044 / Rrim(I) all: 0.086 / Rsym value: 0.073 / Net I/σ(I): 15.39
Reflection shellResolution: 2.8→2.9 Å / Redundancy: 3.3 % / Rmerge(I) obs: 0.458 / Num. unique obs: 8940 / CC1/2: 0.825 / CC star: 0.951 / Rrim(I) all: 0.544 / Rsym value: 0.458 / % possible all: 98.8

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Processing

Software
NameVersionClassification
SCALEPACKdata scaling
REFMAC5.8.0352refinement
PDB_EXTRACT3.27data extraction
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.8→29.7 Å / Cor.coef. Fo:Fc: 0.958 / Cor.coef. Fo:Fc free: 0.929 / SU B: 29.04 / SU ML: 0.239 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.563 / ESU R Free: 0.289 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.221 4563 5 %RANDOM
Rwork0.1705 ---
obs0.173 85840 99.34 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 146.7 Å2 / Biso mean: 60.27 Å2 / Biso min: 22.6 Å2
Baniso -1Baniso -2Baniso -3
1-0.02 Å2-0 Å2-2.1 Å2
2--0.47 Å20 Å2
3---0.53 Å2
Refinement stepCycle: final / Resolution: 2.8→29.7 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms17727 0 0 347 18074
Biso mean---45.85 -
Num. residues----2189
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.01218094
X-RAY DIFFRACTIONr_bond_other_d0.0060.01615979
X-RAY DIFFRACTIONr_angle_refined_deg1.3911.64824401
X-RAY DIFFRACTIONr_angle_other_deg0.4991.56737221
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.38252174
X-RAY DIFFRACTIONr_dihedral_angle_2_deg8.3065166
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.999103142
X-RAY DIFFRACTIONr_chiral_restr0.0620.22578
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0221064
X-RAY DIFFRACTIONr_gen_planes_other0.0070.023844
LS refinement shellResolution: 2.8→2.87 Å / Rfactor Rfree error: 0
RfactorNum. reflection% reflection
Rfree0.31 301 -
Rwork0.279 5812 -
obs--92.52 %
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)
13.2055-0.0566-0.17052.43490.01162.2916-0.133-0.0864-0.12350.27330.0879-0.4276-0.24830.32730.04510.1667-0.0396-0.08340.2168-0.08570.138774.422-24.0439.07
21.5988-0.0889-0.99822.15220.16013.47280.03470.5169-0.0687-0.43280.02660.1487-0.2187-0.3005-0.06130.2366-0.0049-0.08910.3703-0.13490.116455.467-26.37312.16
31.8056-0.2169-0.31452.1367-0.09533.14630.0609-0.2493-0.00460.31710.09470.0503-0.09870.1225-0.15570.16620.0432-0.00920.0649-0.00150.019315.785-22.48384.396
43.8499-0.3893-0.26761.8413-0.18211.10850.1270.4587-0.2959-0.2581-0.10080.457-0.0536-0.2968-0.02620.19410.1014-0.08190.1878-0.02950.1413-5.547-22.70659.21
53.5316-1.52760.30554.0990.41213.2116-0.05420.11150.4916-0.25240.34340.2407-0.5082-0.1256-0.28920.3798-0.07060.05910.20870.10530.190436.3823.41532.425
62.46290.17980.46955.19512.3623.4988-0.17880.2354-0.6422-0.2310.2256-0.02110.46980.1411-0.04680.1772-0.02430.04490.184-0.01760.344520.116-51.81447.214
73.4023-0.61961.90653.1131-1.57063.9732-0.2698-0.0521-0.11230.29740.0193-0.3052-0.42320.37340.25050.23070.0992-0.01570.2999-0.0210.325371.022-45.35360.304
82.73390.73751.23762.66840.09473.95240.2521-0.4483-0.13840.23970.0057-0.1565-0.08090.0055-0.25780.2776-0.04210.04880.232-0.07680.142237.563-0.85284.933
92.9010.5940.42694.762-1.86943.9428-0.1453-0.0923-0.70510.01280.19340.17630.7193-0.0704-0.04810.22420.08550.04550.2255-0.11730.454248.366-54.58149.142
102.6754-1.39632.41892.2284-1.87074.77220.53010.568-0.3805-0.6517-0.0250.14640.59380.2123-0.50510.58220.03-0.05410.39790.03110.175335.016-3.9747.255
113.70682.36650.65094.2313-0.33723.28090.05940.21980.75360.10870.08410.2153-0.69440.0857-0.14340.44030.08660.13180.12250.03970.233531.0976.92660.064
124.13531.77552.52481.42921.51723.4766-0.486-0.01930.327-0.2514-0.10880.7887-0.7164-0.70840.59480.40870.0551-0.14180.3935-0.09180.6838-3.477-45.09938.732
130.38590.0266-0.23270.1142-0.00260.3172-0.03550.016-0.06140.00460.0630.007-0.03040.0298-0.02750.11430.0437-0.0140.1611-0.0180.052635.404-23.89951.519
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A26 - 287
2X-RAY DIFFRACTION2B28 - 287
3X-RAY DIFFRACTION3C25 - 285
4X-RAY DIFFRACTION4D28 - 285
5X-RAY DIFFRACTION5E22 - 160
6X-RAY DIFFRACTION6F21 - 160
7X-RAY DIFFRACTION7G22 - 168
8X-RAY DIFFRACTION8H22 - 168
9X-RAY DIFFRACTION9I21 - 168
10X-RAY DIFFRACTION10J22 - 168
11X-RAY DIFFRACTION11K22 - 168
12X-RAY DIFFRACTION12L22 - 168
13X-RAY DIFFRACTION13A301 - 348
14X-RAY DIFFRACTION13B301 - 337
15X-RAY DIFFRACTION13C301 - 359
16X-RAY DIFFRACTION13D301 - 342
17X-RAY DIFFRACTION13E201 - 222
18X-RAY DIFFRACTION13F201 - 232
19X-RAY DIFFRACTION13G201 - 215
20X-RAY DIFFRACTION13H201 - 219
21X-RAY DIFFRACTION13I201 - 224
22X-RAY DIFFRACTION13J201 - 217
23X-RAY DIFFRACTION13K201 - 222
24X-RAY DIFFRACTION13L201 - 207

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