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- PDB-2rb7: Crystal structure of co-catalytic metallopeptidase (YP_387682.1) ... -

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Basic information

Entry
Database: PDB / ID: 2rb7
TitleCrystal structure of co-catalytic metallopeptidase (YP_387682.1) from Desulfovibrio desulfuricans G20 at 1.60 A resolution
ComponentsPeptidase, M20/M25/M40 familyProtease
KeywordsHYDROLASE / YP_387682.1 / co-catalytic metallopeptidase / Peptidase family M20/M25/M40 / Structural Genomics / Joint Center for Structural Genomics / JCSG / Protein Structure Initiative / PSI
Function / homology
Function and homology information


ArgE / dapE / ACY1 / CPG2 / yscS family signature 1. / ArgE/DapE/ACY1/CPG2/YscS, conserved site / Alpha-Beta Plaits - #360 / Peptidase M20, dimerisation domain / Bacterial exopeptidase dimerisation domain / Peptidase dimerisation domain / Peptidase M20 / Peptidase family M20/M25/M40 / Zn peptidases / Aminopeptidase ...ArgE / dapE / ACY1 / CPG2 / yscS family signature 1. / ArgE/DapE/ACY1/CPG2/YscS, conserved site / Alpha-Beta Plaits - #360 / Peptidase M20, dimerisation domain / Bacterial exopeptidase dimerisation domain / Peptidase dimerisation domain / Peptidase M20 / Peptidase family M20/M25/M40 / Zn peptidases / Aminopeptidase / Alpha-Beta Plaits / 2-Layer Sandwich / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
DI(HYDROXYETHYL)ETHER / TRIETHYLENE GLYCOL / Peptidase M20
Similarity search - Component
Biological speciesDesulfovibrio desulfuricans subsp. desulfuricans str. (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.6 Å
AuthorsJoint Center for Structural Genomics (JCSG)
CitationJournal: To be published
Title: Crystal structure of co-catalytic metallopeptidase (YP_387682.1) from Desulfovibrio desulfuricans G20 at 1.60 A resolution
Authors: Joint Center for Structural Genomics (JCSG)
History
DepositionSep 18, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 2, 2007Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Source and taxonomy / Version format compliance
Revision 1.2Oct 25, 2017Group: Author supporting evidence / Refinement description / Category: pdbx_struct_assembly_auth_evidence / software / Item: _software.classification / _software.name
Revision 1.3Jul 24, 2019Group: Data collection / Derived calculations / Refinement description
Category: software / struct_conn
Item: _software.classification / _software.contact_author ..._software.classification / _software.contact_author / _software.contact_author_email / _software.language / _software.location / _software.name / _software.type / _software.version / _struct_conn.pdbx_leaving_atom_flag
Revision 1.4Jan 25, 2023Group: Database references / Category: database_2 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details
Remark 300 BIOMOLECULE: 1 SEE REMARK 350 FOR THE AUTHOR PROVIDED AND PROGRAM GENERATED ASSEMBLY INFORMATION ... BIOMOLECULE: 1 SEE REMARK 350 FOR THE AUTHOR PROVIDED AND PROGRAM GENERATED ASSEMBLY INFORMATION FOR THE STRUCTURE IN THIS ENTRY. THE REMARK MAY ALSO PROVIDE INFORMATION ON BURIED SURFACE AREA. SIZE EXCLUSION CHROMATOGRAPHY SUPPORTS THE ASSIGNMENT OF A DIMER AS THE SIGNIFICANT OLIGOMERIZATION STATE.
Remark 999 SEQUENCE THE CONSTRUCT WAS EXPRESSED WITH A PURIFICATION TAG MGSDKIHHHHHHENLYFQG. THE TAG WAS ... SEQUENCE THE CONSTRUCT WAS EXPRESSED WITH A PURIFICATION TAG MGSDKIHHHHHHENLYFQG. THE TAG WAS REMOVED WITH TEV PROTEASE LEAVING ONLY A GLYCINE FOLLOWED BY THE TARGET SEQUENCE. THE ALTERNATE START CODON HAS BEEN CHANGED TO AUG DURING CLONING TO MAINTAIN A MET AMINO ACID AT POSITION 1.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Peptidase, M20/M25/M40 family
B: Peptidase, M20/M25/M40 family
hetero molecules


Theoretical massNumber of molelcules
Total (without water)81,7278
Polymers80,9582
Non-polymers7696
Water16,502916
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3390 Å2
MethodPISA
Unit cell
Length a, b, c (Å)53.850, 82.190, 89.340
Angle α, β, γ (deg.)90.000, 91.370, 90.000
Int Tables number4
Space group name H-MP1211
DetailsSIZE EXCLUSION CHROMATOGRAPHY SUPPORTS THE ASSIGNMENT OF A DIMER AS THE SIGNIFICANT OLIGOMERIZATION STATE.

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Components

#1: Protein Peptidase, M20/M25/M40 family / Protease


Mass: 40478.816 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Desulfovibrio desulfuricans subsp. desulfuricans str. (bacteria)
Species: Desulfovibrio desulfuricans / Strain: G20 / Gene: YP_387682.1, Dde_1186 / Plasmid: speedET / Production host: Escherichia coli (E. coli) / Strain (production host): HK100 / References: UniProt: Q313A9
#2: Chemical ChemComp-PGE / TRIETHYLENE GLYCOL / Polyethylene glycol


Mass: 150.173 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H14O4
#3: Chemical
ChemComp-PEG / DI(HYDROXYETHYL)ETHER / Diethylene glycol


Mass: 106.120 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C4H10O3
#4: Chemical ChemComp-PG4 / TETRAETHYLENE GLYCOL / Polyethylene glycol


Mass: 194.226 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H18O5 / Comment: precipitant*YM
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 916 / 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: 2.44 Å3/Da / Density % sol: 49.62 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 7.1
Details: NANODROP, 0.2M Sodium fluoride, 20.0% PEG 3350, No Buffer pH 7.1, 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: 0.91837, 0.97901, 0.97926
DetectorType: MARMOSAIC 325 mm CCD / Detector: CCD / Date: Jun 3, 2007 / Details: Flat mirror (vertical focusing)
RadiationMonochromator: Single crystal Si(111) bent (horizontal focusing)
Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.918371
20.979011
30.979261
ReflectionResolution: 1.6→27.995 Å / Num. obs: 101945 / % possible obs: 98.7 % / Observed criterion σ(I): -3 / Redundancy: 3.28 % / Biso Wilson estimate: 18.5 Å2 / Rmerge(I) obs: 0.045 / Net I/σ(I): 9.92
Reflection shell
Resolution (Å)Rmerge(I) obsMean I/σ(I) obsNum. measured obsDiffraction-ID% possible all
1.6-1.660.3142.228804194.5
1.66-1.720.2612.830168199.5
1.72-1.80.2133.434334199.5
1.8-1.90.1654.535319199.4
1.9-2.020.1126.633788199.2
2.02-2.170.0769.432642199.5
2.17-2.390.05812.234446199.4
2.39-2.730.04515.134248199.3
2.73-3.440.0341934856199
3.44-27.9950.02523.935411197.8

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Phasing

PhasingMethod: MAD

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Processing

Software
NameVersionClassificationNB
REFMAC5.2.0019refinement
PHENIXrefinement
SOLVEphasing
MolProbity3beta29model building
XSCALEdata scaling
PDB_EXTRACT3data extraction
MAR345CCDdata collection
XDSdata reduction
RefinementMethod to determine structure: MAD / Resolution: 1.6→27.995 Å / Cor.coef. Fo:Fc: 0.97 / Cor.coef. Fo:Fc free: 0.96 / SU B: 2.979 / SU ML: 0.052 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.078 / ESU R Free: 0.078
Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES
Details: 1. HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. 2. A MET-INHIBITION PROTOCOL WAS USED FOR SELENOMETHIONINE INCORPORATION DURING PROTEIN EXPRESSION. THE OCCUPANCY OF THE SE ATOMS IN THE ...Details: 1. HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. 2. 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 TO ACCOUNT FOR THE REDUCED SCATTERING POWER DUE TO PARTIAL S-MET INCORPORATION. 3. ATOM RECORD CONTAINS RESIDUAL B FACTORS ONLY. 4. RESIDUES 360-363 IN CHAINS A,B ARE DISORDERED AND HAVE NOT BEEN MODELLED. 5. FOUR PEG, ONE PGE AND ONE PG4 MOLECULE(S) HAVE BEEN MODELED AS PART OF THE SOLVENT STRUCTURE.
RfactorNum. reflection% reflectionSelection details
Rfree0.18 5090 5 %RANDOM
Rwork0.154 ---
obs0.155 101918 99.4 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 14.803 Å2
Baniso -1Baniso -2Baniso -3
1-0.46 Å20 Å2-0.75 Å2
2--0.17 Å20 Å2
3----0.67 Å2
Refinement stepCycle: LAST / Resolution: 1.6→27.995 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5505 0 51 916 6472
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0170.0225985
X-RAY DIFFRACTIONr_bond_other_d0.0020.024151
X-RAY DIFFRACTIONr_angle_refined_deg1.6241.9698146
X-RAY DIFFRACTIONr_angle_other_deg1.007310150
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.6145820
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.95323.467274
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.784151072
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.971557
X-RAY DIFFRACTIONr_chiral_restr0.1030.2908
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.026785
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021206
X-RAY DIFFRACTIONr_nbd_refined0.2240.21155
X-RAY DIFFRACTIONr_nbd_other0.210.24754
X-RAY DIFFRACTIONr_nbtor_refined0.1690.22844
X-RAY DIFFRACTIONr_nbtor_other0.0870.23266
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1640.2683
X-RAY DIFFRACTIONr_xyhbond_nbd_other0.1170.21
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1790.222
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2560.289
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1970.255
X-RAY DIFFRACTIONr_mcbond_it2.19934078
X-RAY DIFFRACTIONr_mcbond_other0.54831530
X-RAY DIFFRACTIONr_mcangle_it2.64256001
X-RAY DIFFRACTIONr_scbond_it4.74682431
X-RAY DIFFRACTIONr_scangle_it6.736112093
LS refinement shellResolution: 1.6→1.641 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.257 361 -
Rwork0.221 6844 -
all-7205 -
obs--95.08 %
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)
10.30920.09770.03380.7631-0.0990.6313-0.0080.0098-0.0214-0.00010.0217-0.0323-0.013-0.0227-0.0138-0.03130.0036-0.008-0.0373-0.0072-0.030822.189639.432364.8384
21.22170.07620.32530.2937-0.1660.7252-0.0361-0.13510.029-0.01410.0386-0.0370.015-0.0138-0.0025-0.05950.01390.0023-0.0255-0.0199-0.039634.195126.462596.0425
30.5329-0.1338-0.18920.78220.19410.91690.04610.02330.0426-0.0703-0.00360.0125-0.0887-0.0827-0.04250.00710.0083-0.0039-0.01430.0035-0.019770.267644.23118.6992
41.6797-0.28781.37130.4364-0.23161.11950.01760.0358-0.13210.04730.00090.03520.0229-0.0868-0.0185-0.04860.00850.01210.0281-0.0142-0.007653.468222.517294.9299
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA0 - 1741 - 175
2X-RAY DIFFRACTION1AA280 - 359281 - 360
3X-RAY DIFFRACTION2AA175 - 279176 - 280
4X-RAY DIFFRACTION3BB0 - 1741 - 175
5X-RAY DIFFRACTION3BB280 - 359281 - 360
6X-RAY DIFFRACTION4BB175 - 279176 - 280

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