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- PDB-3fdg: The crystal structure of the dipeptidase AC, Metallo peptidase. M... -

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Basic information

Entry
Database: PDB / ID: 3fdg
TitleThe crystal structure of the dipeptidase AC, Metallo peptidase. MEROPS family M19
ComponentsDipeptidase AC. Metallo peptidase. MEROPS family M19
KeywordsHYDROLASE / dipeptidase AC / Metallo peptidase. MEROPS family M19 / structural genomics / MCSG / PSI-2 / Protein Structure Initiative / Midwest Center for Structural Genomics
Function / homology
Function and homology information


membrane dipeptidase / metallodipeptidase activity / proteolysis / metal ion binding
Similarity search - Function
Peptidase M19 / Membrane dipeptidase (Peptidase family M19) / Renal dipeptidase family profile. / Metal-dependent hydrolases / Metal-dependent hydrolase / TIM Barrel / Alpha-Beta Barrel / Alpha Beta
Similarity search - Domain/homology
Biological speciesRhodobacter sphaeroides (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.8 Å
AuthorsZhang, R. / Hatzos, C. / Freeman, L. / Joachimiak, A. / Midwest Center for Structural Genomics (MCSG)
CitationJournal: To be Published
Title: The crystal structure of the dipeptidase AC, Metallo peptidase. MEROPS family M19
Authors: Zhang, R. / Hatzos, C. / Freeman, L. / Joachimiak, A.
History
DepositionNov 25, 2008Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 23, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Refinement description ...Advisory / Refinement description / Source and taxonomy / Version format compliance
Revision 1.2Nov 1, 2017Group: Refinement description / Category: software
Revision 1.3Dec 27, 2023Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Dipeptidase AC. Metallo peptidase. MEROPS family M19
B: Dipeptidase AC. Metallo peptidase. MEROPS family M19
hetero molecules


Theoretical massNumber of molelcules
Total (without water)78,1706
Polymers78,0732
Non-polymers974
Water8,071448
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2090 Å2
ΔGint-57 kcal/mol
Surface area23930 Å2
MethodPISA
Unit cell
Length a, b, c (Å)46.246, 50.683, 81.594
Angle α, β, γ (deg.)82.42, 73.61, 68.18
Int Tables number1
Space group name H-MP1
DetailsThis protein existed as dimer. The deposited MolA and MolB represent the dimer in the asymmetric unit.

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Components

#1: Protein Dipeptidase AC. Metallo peptidase. MEROPS family M19


Mass: 39036.496 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rhodobacter sphaeroides (bacteria) / Strain: 2.4.1 / Gene: GI:77388796, RHOS4_24130, RSP_0802 / Plasmid: pMCSG19 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 / References: UniProt: Q3IZQ3
#2: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Mg
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 448 / 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: 2.18 Å3/Da / Density % sol: 43.6 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: 0.2M Magnesium chloride hexahydrate, 0.1M Tris, 25% w/v Polyethylene glycol 3350, pH 8.5, VAPOR DIFFUSION, SITTING DROP, temperature 289K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.9794, 0.9796
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Nov 6, 2008 / Details: mirrors
RadiationMonochromator: Si 111 channel / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.97941
20.97961
ReflectionResolution: 1.8→78.33 Å / Num. all: 57863 / Num. obs: 52476 / % possible obs: 90.69 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 2.5 % / Biso Wilson estimate: 22.3 Å2 / Rmerge(I) obs: 0.093 / Net I/σ(I): 16.48
Reflection shellResolution: 1.8→1.848 Å / Redundancy: 2.2 % / Rmerge(I) obs: 0.27 / Mean I/σ(I) obs: 2.44 / Num. unique all: 4494 / % possible all: 55.18

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Processing

Software
NameVersionClassification
SBC-Collectdata collection
HKL-3000phasing
REFMAC5.5.0054refinement
HKL-3000data reduction
HKL-3000data scaling
RefinementMethod to determine structure: MAD / Resolution: 1.8→78.33 Å / Cor.coef. Fo:Fc: 0.959 / Cor.coef. Fo:Fc free: 0.934 / SU B: 6.397 / SU ML: 0.09 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.147 / ESU R Free: 0.14
Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.2226 2814 5.1 %RANDOM
Rwork0.17531 ---
obs0.17779 52476 90.69 %-
all-57863 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 21.335 Å2
Baniso -1Baniso -2Baniso -3
1--0.6 Å2-0.67 Å20.12 Å2
2--2.86 Å21.12 Å2
3----2.12 Å2
Refinement stepCycle: LAST / Resolution: 1.8→78.33 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5296 0 4 448 5748
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.020.0215421
X-RAY DIFFRACTIONr_angle_refined_deg1.8371.9557339
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.2175682
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.07822.213253
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.48915864
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.6091558
X-RAY DIFFRACTIONr_chiral_restr0.1710.2779
X-RAY DIFFRACTIONr_gen_planes_refined0.010.0214218
X-RAY DIFFRACTIONr_mcbond_it0.9821.53396
X-RAY DIFFRACTIONr_mcangle_it1.6825400
X-RAY DIFFRACTIONr_scbond_it3.20732025
X-RAY DIFFRACTIONr_scangle_it4.9464.51939
LS refinement shellResolution: 1.802→1.848 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.298 121 -
Rwork0.246 2359 -
obs-2480 55.18 %
Refinement TLS params.Method: refined / Origin x: 57.125 Å / Origin y: 39.808 Å / Origin z: 9.349 Å
111213212223313233
T0.0568 Å2-0.0212 Å20.0059 Å2-0.0347 Å2-0.006 Å2--0.0777 Å2
L0.3815 °2-0.1315 °20.0652 °2-0.0975 °2-0.1863 °2--0.9681 °2
S0.0384 Å °0.0159 Å °-0.0105 Å °-0.0066 Å °0.0021 Å °0.0175 Å °-0.0093 Å °0.0821 Å °-0.0405 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A3 - 50
2X-RAY DIFFRACTION1A51 - 100
3X-RAY DIFFRACTION1A101 - 150
4X-RAY DIFFRACTION1A151 - 200
5X-RAY DIFFRACTION1A201 - 250
6X-RAY DIFFRACTION1A251 - 300
7X-RAY DIFFRACTION1A301 - 355
8X-RAY DIFFRACTION1B3 - 50
9X-RAY DIFFRACTION1B51 - 100
10X-RAY DIFFRACTION1B101 - 150
11X-RAY DIFFRACTION1B151 - 200
12X-RAY DIFFRACTION1B201 - 250
13X-RAY DIFFRACTION1B251 - 300
14X-RAY DIFFRACTION1B301 - 355

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