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- PDB-4fdy: Crystal structure of a similar to lipoprotein, NLP/P60 family (SA... -

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Basic information

Entry
Database: PDB / ID: 4fdy
TitleCrystal structure of a similar to lipoprotein, NLP/P60 family (SAV0400) from Staphylococcus aureus subsp. aureus Mu50 at 2.23 A resolution
ComponentsSimilar to lipoprotein, NLP/P60 family
KeywordsHYDROLASE / Slt/lysozyme-like muramidase / NlpC/P60 LD endopeptidase / Structural Genomics / Joint Center for Structural Genomics / JCSG / Protein Structure Initiative / PSI-BIOLOGY
Function / homology
Function and homology information


cysteine-type peptidase activity
Similarity search - Function
: / Lysozyme-like / : / NlpC/P60 family / NlpC/P60 domain profile. / Endopeptidase, NLPC/P60 domain / endopeptidase domain like (from Nostoc punctiforme) / endopeptidase fold (from Nostoc punctiforme) / Lysozyme - #10 / Papain-like cysteine peptidase superfamily ...: / Lysozyme-like / : / NlpC/P60 family / NlpC/P60 domain profile. / Endopeptidase, NLPC/P60 domain / endopeptidase domain like (from Nostoc punctiforme) / endopeptidase fold (from Nostoc punctiforme) / Lysozyme - #10 / Papain-like cysteine peptidase superfamily / Lysozyme / Lysozyme-like domain superfamily / Alpha-Beta Complex / Orthogonal Bundle / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
Similar to lipoprotein, NLP/P60 family / Similar to lipoprotein, NLP/P60 family
Similarity search - Component
Biological speciesStaphylococcus aureus subsp. aureus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.23 Å
AuthorsJoint Center for Structural Genomics (JCSG)
CitationJournal: J.Mol.Biol. / Year: 2014
Title: Structures of a Bifunctional Cell Wall Hydrolase CwlT Containing a Novel Bacterial Lysozyme and an NlpC/P60 dl-Endopeptidase.
Authors: Xu, Q. / Chiu, H.J. / Farr, C.L. / Jaroszewski, L. / Knuth, M.W. / Miller, M.D. / Lesley, S.A. / Godzik, A. / Elsliger, M.A. / Deacon, A.M. / Wilson, I.A.
History
DepositionMay 29, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 25, 2012Provider: repository / Type: Initial release
Revision 1.1Dec 4, 2013Group: Database references
Revision 1.2Jan 8, 2014Group: Database references
Revision 1.3Nov 15, 2017Group: Refinement description / Category: software
Revision 1.4Feb 1, 2023Group: Database references / Derived calculations / Category: database_2 / struct_conn / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Similar to lipoprotein, NLP/P60 family
B: Similar to lipoprotein, NLP/P60 family


Theoretical massNumber of molelcules
Total (without water)69,9912
Polymers69,9912
Non-polymers00
Water3,621201
1
A: Similar to lipoprotein, NLP/P60 family


Theoretical massNumber of molelcules
Total (without water)34,9951
Polymers34,9951
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Similar to lipoprotein, NLP/P60 family


Theoretical massNumber of molelcules
Total (without water)34,9951
Polymers34,9951
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)40.666, 71.994, 124.917
Angle α, β, γ (deg.)90.000, 95.910, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Similar to lipoprotein, NLP/P60 family


Mass: 34995.492 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Staphylococcus aureus subsp. aureus (bacteria)
Strain: Mu50 / Gene: SAV0400 / Plasmid: SpeedET / Production host: Escherichia Coli (E. coli) / Strain (production host): PB1 / References: UniProt: Q932I6, UniProt: A0A0H3JPP0*PLUS
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 201 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsTHE CONSTRUCT (29-340) WAS EXPRESSED WITH A PURIFICATION TAG MGSDKIHHHHHHENLYFQG. THE TAG WAS ...THE CONSTRUCT (29-340) WAS EXPRESSED WITH A PURIFICATION TAG MGSDKIHHHHHHENLYFQG. THE TAG WAS REMOVED WITH TEV PROTEASE LEAVING ONLY A GLYCINE (0) FOLLOWED BY THE TARGET SEQUENCE.

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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: 2.6 Å3/Da / Density % sol: 52.67 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 6
Details: 0.2M calcium acetate, 20.0% polyethylene glycol 8000, 0.1M MES pH 6.0, NANODROP, VAPOR DIFFUSION, SITTING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL11-1 / Wavelength: 0.97895,0.91837,0.97853
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Apr 5, 2012
Details: Flat mirror (vertical focusing); single crystal Si(111) bent monochromator (horizontal focusing)
RadiationMonochromator: single crystal Si(111) bent / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.978951
20.918371
30.978531
ReflectionResolution: 2.23→47.035 Å / Num. obs: 33428 / % possible obs: 94.9 % / Observed criterion σ(I): -3 / Biso Wilson estimate: 53.501 Å2 / Rmerge(I) obs: 0.052 / Net I/σ(I): 12.6
Reflection shell

Diffraction-ID: 1

Resolution (Å)Highest resolution (Å)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. unique obs% possible all
2.23-2.310.7191.711881337196.7
2.31-2.40.5372.211588332696.3
2.4-2.510.4012.911479333496.2
2.51-2.640.2734.211062319893.2
2.64-2.810.176.712342349297.2
2.81-3.020.10310.211344330396.5
3.02-3.330.06315.311249331692.4
3.33-3.810.0422.811553336396
3.81-4.780.0329.110945323592.5
4.780.033111135338192

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Phasing

PhasingMethod: MAD

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Processing

Software
NameVersionClassificationNB
MolProbity3beta29model building
PDB_EXTRACT3.1data extraction
SHELXphasing
SHARPphasing
XSCALEDecember 29, 2011data scaling
BUSTER-TNT2.10.0refinement
XDSdata reduction
SHELXDphasing
BUSTER2.10.0refinement
RefinementMethod to determine structure: MAD / Resolution: 2.23→47.035 Å / Cor.coef. Fo:Fc: 0.953 / Cor.coef. Fo:Fc free: 0.9368 / Occupancy max: 1 / Occupancy min: 0.5 / Cross valid method: THROUGHOUT / σ(F): 0
Details: 1. A MET-INHIBITION PROTOCOL WAS USED FOR SELENOMETHIONINE INCORPORATION DURING PROTEIN EXPRESSION. THE OCCUPANCY OF THE SE ATOMS IN THE MSE RESIDUES WAS REDUCED TO 0.75 FOR THE REDUCED ...Details: 1. A MET-INHIBITION PROTOCOL WAS USED FOR SELENOMETHIONINE INCORPORATION DURING PROTEIN EXPRESSION. THE OCCUPANCY OF THE SE ATOMS IN THE MSE RESIDUES WAS REDUCED TO 0.75 FOR THE REDUCED SCATTERING POWER DUE TO PARTIAL S-MET INCORPORATION. 2. ATOM RECORD CONTAINS SUM OF TLS AND RESIDUAL B FACTORS. ANISOU RECORD CONTAINS SUM OF TLS AND RESIDUAL U FACTORS. 3. THE MAD PHASES WERE USED AS RESTRAINTS DURING REFINEMENT. 4. NCS RESTRAINTS WERE APPLIED USING BUSTER'S LSSR RESTRAINT REPRESENTATION (-AUTONCS). 5. THE DENSITY FOR THE N-TERMINUS OF B CHAIN (46-71) IS POOR, THE MODEL FOR THIS REGION IS BASED ON A CHAIN.
RfactorNum. reflection% reflectionSelection details
Rfree0.2418 1677 5.02 %RANDOM
Rwork0.1985 ---
obs0.2006 33396 95.03 %-
Displacement parametersBiso max: 168.04 Å2 / Biso mean: 65.5059 Å2 / Biso min: 32.07 Å2
Baniso -1Baniso -2Baniso -3
1--4.8848 Å20 Å24.5731 Å2
2--2.0488 Å20 Å2
3---2.8361 Å2
Refine analyzeLuzzati coordinate error obs: 0.408 Å
Refinement stepCycle: LAST / Resolution: 2.23→47.035 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4648 0 0 201 4849
Refine LS restraints
Refine-IDTypeNumberRestraint functionWeightDev ideal
X-RAY DIFFRACTIONt_dihedral_angle_d2129SINUSOIDAL4
X-RAY DIFFRACTIONt_trig_c_planes136HARMONIC2
X-RAY DIFFRACTIONt_gen_planes705HARMONIC5
X-RAY DIFFRACTIONt_it4798HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_chiral_improper_torsion602SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact5793SEMIHARMONIC4
X-RAY DIFFRACTIONt_bond_d4798HARMONIC20.01
X-RAY DIFFRACTIONt_angle_deg6536HARMONIC21.04
X-RAY DIFFRACTIONt_omega_torsion3.33
X-RAY DIFFRACTIONt_other_torsion2.47
LS refinement shellResolution: 2.23→2.3 Å / Total num. of bins used: 17
RfactorNum. reflection% reflection
Rfree0.2249 149 5.12 %
Rwork0.2262 2759 -
all0.2261 2908 -
obs--95.03 %
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)
12.19450.22080.94343.29140.82833.74390.11410.05350.30060.26120.0779-0.2023-0.21830.5527-0.192-0.1393-0.0406-0.0536-0.0727-0.0569-0.110522.72027.1129-42.8707
23.32940.77792.46753.24751.26293.74620.2298-0.004-0.40340.58270.024-0.3430.5958-0.0331-0.25380.1048-0.0354-0.1337-0.2548-0.0248-0.101248.9313-23.2303-51.3675
32.08890.59772.53523.41760.67965.043-0.1845-0.12350.2316-0.44470.00990.5011-0.5418-0.55990.1746-0.120.0828-0.0888-0.06840.0321-0.17543.8835.1864-19.7324
42.3211-0.79381.49773.8783-2.20644.17380.11420.159-0.118-0.5590.00110.11430.57260.0523-0.11540.10260.0206-0.1062-0.1939-0.0053-0.173519.17315.4271-10.3206
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1{A|46 - 208}A46 - 208
2X-RAY DIFFRACTION2{A|209 - 340}A209 - 340
3X-RAY DIFFRACTION3{B|46 - 208}B46 - 208
4X-RAY DIFFRACTION4{B|209 - 340}B209 - 340

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