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- PDB-4hpe: Crystal structure of a putative cell wall hydrolase (CD630_03720)... -

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Basic information

Entry
Database: PDB / ID: 4hpe
TitleCrystal structure of a putative cell wall hydrolase (CD630_03720) from Clostridium difficile 630 at 2.38 A resolution
ComponentsPutative cell wall hydrolase Tn916-like,CTn1-Orf17
KeywordsHYDROLASE / Two domains protein / 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
Cell wall hydrolase Tn916-like,CTn1-Orf17
Similarity search - Component
Biological speciesClostridium difficile (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.38 Å
AuthorsJoint Center for Structural Genomics (JCSG)
CitationJournal: To be published
Title: Crystal structure of a putative cell wall hydrolase (CD630_03720) from Clostridium difficile 630 at 2.38 A resolution
Authors: Joint Center for Structural Genomics (JCSG)
History
DepositionOct 23, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 28, 2012Provider: repository / Type: Initial release
Revision 1.1Nov 15, 2017Group: Refinement description / Category: software / Item: _software.classification / _software.name
Revision 1.2Feb 1, 2023Group: Database references / Derived calculations
Category: database_2 / struct_conn ...database_2 / struct_conn / struct_ref_seq_dif / struct_site
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 / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.3Sep 20, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.4Dec 6, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond / Item: _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_2

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Putative cell wall hydrolase Tn916-like,CTn1-Orf17
B: Putative cell wall hydrolase Tn916-like,CTn1-Orf17
C: Putative cell wall hydrolase Tn916-like,CTn1-Orf17
D: Putative cell wall hydrolase Tn916-like,CTn1-Orf17
E: Putative cell wall hydrolase Tn916-like,CTn1-Orf17
F: Putative cell wall hydrolase Tn916-like,CTn1-Orf17
hetero molecules


Theoretical massNumber of molelcules
Total (without water)203,83819
Polymers203,1516
Non-polymers68713
Water10,629590
1
A: Putative cell wall hydrolase Tn916-like,CTn1-Orf17
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,1847
Polymers33,8581
Non-polymers3266
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Putative cell wall hydrolase Tn916-like,CTn1-Orf17
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,9863
Polymers33,8581
Non-polymers1282
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Putative cell wall hydrolase Tn916-like,CTn1-Orf17
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,8942
Polymers33,8581
Non-polymers351
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
4
D: Putative cell wall hydrolase Tn916-like,CTn1-Orf17
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,9863
Polymers33,8581
Non-polymers1282
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
5
E: Putative cell wall hydrolase Tn916-like,CTn1-Orf17
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,8942
Polymers33,8581
Non-polymers351
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
6
F: Putative cell wall hydrolase Tn916-like,CTn1-Orf17
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,8942
Polymers33,8581
Non-polymers351
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)65.522, 101.211, 101.436
Angle α, β, γ (deg.)109.710, 108.860, 101.360
Int Tables number1
Space group name H-MP1

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Components

#1: Protein
Putative cell wall hydrolase Tn916-like,CTn1-Orf17


Mass: 33858.453 Da / Num. of mol.: 6 / Fragment: UNP residues 29-335
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Clostridium difficile (bacteria) / Strain: 630 / Gene: CD630_03720, YP_001086839.1 / Plasmid: SpeedET / Production host: Escherichia coli (E. coli) / Strain (production host): HK100 / References: UniProt: Q18DB2
#2: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: Cl
#3: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 590 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsTHE CONSTRUCT (29-335) WAS EXPRESSED WITH A PURIFICATION TAG MGSDKIHHHHHHENLYFQG. THE TAG WAS ...THE CONSTRUCT (29-335) 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: 2.77 Å3/Da / Density % sol: 55.6 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 5.1
Details: 20.00% 2-propanol, 24.00% polyethylene glycol 4000, 0.1M sodium citrate - citric acid pH 5.1, NANODROP, VAPOR DIFFUSION, SITTING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL12-2 / Wavelength: 0.9794
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jul 17, 2012
Details: Rhodium-coated vertical and horizontal focusing mirrors; liquid-nitrogen cooled double crystal Si(111) monochromator
RadiationMonochromator: double crystal Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9794 Å / Relative weight: 1
ReflectionResolution: 2.38→49.396 Å / Num. obs: 76631 / % possible obs: 84.9 % / Observed criterion σ(I): -3 / Biso Wilson estimate: 48.904 Å2 / Rmerge(I) obs: 0.084 / Net I/σ(I): 6.53
Reflection shell
Resolution (Å)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. unique obsDiffraction-ID% possible all
2.38-2.460.4971.62529713065178.9
2.46-2.560.4251.93181516077189.9
2.56-2.680.3072.53173416048188.5
2.68-2.820.2283.32834714427182.9
2.82-30.1614.53130615823188.7
3-3.230.1166.23015915275187.9
3.23-3.550.0857.92804214258182.5
3.55-4.060.06210.92951414931184.7
4.06-5.10.05213.12819414350182
5.1-49.3960.04713.92900214737182.6

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
MolProbity3beta29model building
PDB_EXTRACT3.1data extraction
PHASER2.3.0phasing
XSCALEMarch 15, 2012data scaling
BUSTER-TNTrefinement
XDSdata reduction
BUSTER2.10.0refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4FDY

4fdy


Resolution: 2.38→49.396 Å / Cor.coef. Fo:Fc: 0.9441 / Cor.coef. Fo:Fc free: 0.9278 / 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. CL AND GOL MODELED ARE PRESENT IN PROTEIN/CRYO CONDITIONS. 4. NCS RESTRAINTS WERE APPLIED USING BUSTER'S LSSR RESTRAINT REPRESENTATION (-AUTONCS). 5. CYS242 IS OXIDIZED (OCS) BASED ON ELECTRON DENSITY.
RfactorNum. reflection% reflectionSelection details
Rfree0.2108 3897 5.09 %RANDOM
Rwork0.1746 ---
obs0.1764 76620 87.62 %-
Displacement parametersBiso max: 139.82 Å2 / Biso mean: 50.0773 Å2 / Biso min: 21.88 Å2
Baniso -1Baniso -2Baniso -3
1--7.4964 Å21.7899 Å23.6459 Å2
2--1.2662 Å20.7264 Å2
3---6.2302 Å2
Refine analyzeLuzzati coordinate error obs: 0.325 Å
Refinement stepCycle: LAST / Resolution: 2.38→49.396 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms13311 0 33 590 13934
Refine LS restraints
Refine-IDTypeNumberRestraint functionWeightDev ideal
X-RAY DIFFRACTIONt_dihedral_angle_d6078SINUSOIDAL2
X-RAY DIFFRACTIONt_trig_c_planes361HARMONIC2
X-RAY DIFFRACTIONt_gen_planes2011HARMONIC5
X-RAY DIFFRACTIONt_it13685HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_chiral_improper_torsion1673SEMIHARMONIC5
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_contact15948SEMIHARMONIC4
X-RAY DIFFRACTIONt_bond_d13685HARMONIC20.01
X-RAY DIFFRACTIONt_angle_deg18559HARMONIC21.03
X-RAY DIFFRACTIONt_omega_torsion3.23
X-RAY DIFFRACTIONt_other_torsion2.73
LS refinement shellResolution: 2.38→2.44 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.2399 267 5.26 %
Rwork0.2028 4805 -
all0.2048 5072 -
obs--87.62 %
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)
10.5531-0.15060.13281.3434-0.55461.119-0.0508-0.0692-0.02270.0986-0.0651-0.0931-0.10840.10610.1160.15820.1007-0.0082-0.10050.075-0.108155.5142.6826-48.1151
21.71770.09450.65171.9407-0.13332.84390.04790.2420.0590.1031-0.216-0.4924-0.16870.48460.16810.05660.0869-0.0354-0.0630.1181-0.100358.768827.8097-70.4707
31.4567-0.78581.15172.7885-1.23942.09150.0358-0.01590.0160.33280.02720.0766-0.04650.0089-0.0630.21580.14940.0775-0.19360.0505-0.193434.991538.0744-68.799
41.4896-0.19790.07872.4737-0.01781.6373-0.019-0.0657-0.07250.23650.02850.4853-0.1712-0.2972-0.00960.140.1920.1264-0.14510.0773-0.083530.73078.5948-52.6701
50.63140.36090.01940.6925-0.36021.4763-0.04320.00910.0191-0.00180.05630.04240.0842-0.1635-0.01310.09370.0860.1133-0.04610.0743-0.095525.4518-28.14-62.5314
62.61320.62310.21113.0066-0.42252.32650.08810.09260.0838-0.21630.00540.23830.3077-0.4559-0.09360.1024-0.05470.0182-0.00390.1152-0.244922.1192-26.3928-95.9628
70.86930.3281.01182.24661.2974.5936-0.0750.04210.2009-0.01490.098-0.2705-0.35550.5191-0.0231-0.05790.09010.0892-0.03510.0857-0.110423.8142-10.3058-21.9531
81.75990.0349-0.9781.8592-0.73042.7591-0.1251-0.228-0.2647-0.0620.0228-0.16950.33560.23980.10230.03510.15930.1269-0.0290.106-0.105616.9954-41.5729-32.9324
91.05670.8730.49685.3561-0.31112.2323-0.0186-0.0882-0.0594-0.1520.09030.54220.306-0.4308-0.0717-0.09230.05650.05880.02590.0892-0.163856.9603-40.1766-35.9554
102.2197-0.63630.67481.803-0.78143.2095-0.0162-0.21240.11530.10580.04670.1566-0.2772-0.3965-0.03040.01360.19660.0748-0.00740.0429-0.127963.6967-11.7331-18.9842
111.02050.6018-0.42043.397-1.7735.1954-0.00060.2563-0.0999-0.485-0.0044-0.18310.39750.22160.0050.23210.15560.1731-0.23190.0194-0.304258.602323.7975-16.6521
120.7824-0.22610.15632.7530.00371.68230.0276-0.08880.1544-0.0721-0.0116-0.4596-0.00560.2575-0.0160.06860.13450.102-0.11080.0421-0.03762.992829.712316.3272
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1{A|43 - 205}A43 - 205
2X-RAY DIFFRACTION2{A|210 - 335}A210 - 335
3X-RAY DIFFRACTION3{B|43 - 205}B43 - 205
4X-RAY DIFFRACTION4{B|210 - 335}B210 - 335
5X-RAY DIFFRACTION5{C|43 - 205}C43 - 205
6X-RAY DIFFRACTION6{C|210 - 335}C210 - 335
7X-RAY DIFFRACTION7{D|43 - 205}D43 - 205
8X-RAY DIFFRACTION8{D|210 - 335}D210 - 335
9X-RAY DIFFRACTION9{E|43 - 205}E43 - 205
10X-RAY DIFFRACTION10{E|210 - 335}E210 - 335
11X-RAY DIFFRACTION11{F|43 - 205}F43 - 205
12X-RAY DIFFRACTION12{F|210 - 335}F210 - 335

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