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- PDB-3peb: The Structure of a Creatine_N Superfamily domain of a dipeptidase... -

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Basic information

Entry
Database: PDB / ID: 3peb
TitleThe Structure of a Creatine_N Superfamily domain of a dipeptidase from Streptococcus thermophilus.
ComponentsDipeptidase
KeywordsHYDROLASE / Structural Genomics / PSI-2 / Protein Structure Initiative / Midwest Center for Structural Genomics / MCSG / Creatinase_N domain / pfam01321 / stu0629
Function / homology
Function and homology information


hydrolase activity / metal ion binding
Similarity search - Function
: / Creatinase, N-terminal / Creatinase/Prolidase N-terminal domain / Peptidase M24B, X-Pro dipeptidase/aminopeptidase P, conserved site / Aminopeptidase P and proline dipeptidase signature. / Creatine Amidinohydrolase; Chain A, domain 1 / Creatinase/prolidase N-terminal domain / Creatinase/Aminopeptidase P/Spt16, N-terminal / Peptidase M24 / Metallopeptidase family M24 ...: / Creatinase, N-terminal / Creatinase/Prolidase N-terminal domain / Peptidase M24B, X-Pro dipeptidase/aminopeptidase P, conserved site / Aminopeptidase P and proline dipeptidase signature. / Creatine Amidinohydrolase; Chain A, domain 1 / Creatinase/prolidase N-terminal domain / Creatinase/Aminopeptidase P/Spt16, N-terminal / Peptidase M24 / Metallopeptidase family M24 / Creatinase/aminopeptidase-like / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Biological speciesStreptococcus thermophilus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.86 Å
AuthorsCuff, M.E. / Mack, J.C. / Clancy, S. / Joachimiak, A. / Midwest Center for Structural Genomics (MCSG)
CitationJournal: TO BE PUBLISHED
Title: The Structure of a Creatine_N Superfamily domain of a dipeptidase from Streptococcus thermophilus.
Authors: Cuff, M.E. / Mack, J.C. / Clancy, S. / Joachimiak, A.
History
DepositionOct 25, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 3, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 8, 2017Group: Refinement description / Category: software
Revision 1.3Nov 27, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / pdbx_struct_conn_angle / 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 / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _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_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_ref_seq_dif.details / _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

Downloads & links

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Assembly

Deposited unit
A: Dipeptidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)16,69014
Polymers15,8171
Non-polymers87413
Water2,882160
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)70.503, 70.503, 160.388
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number178
Space group name H-MP6122
Components on special symmetry positions
IDModelComponents
11A-151-

HOH

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Components

#1: Protein Dipeptidase


Mass: 15816.548 Da / Num. of mol.: 1 / Fragment: N-terminal domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptococcus thermophilus (bacteria) / Strain: LMG 18311 / Gene: pepQ, stu0629 / Plasmid: pMCSG7 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 / References: UniProt: Q5M567
#2: Chemical ChemComp-NHE / 2-[N-CYCLOHEXYLAMINO]ETHANE SULFONIC ACID / N-CYCLOHEXYLTAURINE / CHES


Mass: 207.290 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H17NO3S / Comment: pH buffer*YM
#3: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: C2H6O2
#4: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Na
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 160 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 3.64 Å3/Da / Density % sol: 66.19 %
Crystal growTemperature: 297 K / Method: vapor diffusion, sitting drop / pH: 9.5
Details: 0.1M CHES pH 9.5, 1.0M Sodium Citrate, VAPOR DIFFUSION, SITTING DROP, temperature 297K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-BM / Wavelength: 0.97937 Å
DetectorType: ADSC QUANTUM 210r / Detector: CCD / Date: Jun 14, 2010
RadiationMonochromator: SAGITALLY FOCUSED Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97937 Å / Relative weight: 1
ReflectionRedundancy: 23.8 % / Av σ(I) over netI: 64.13 / Number: 486484 / Rmerge(I) obs: 0.074 / Χ2: 1.59 / D res high: 1.85 Å / D res low: 50 Å / Num. obs: 20449 / % possible obs: 99.4
Diffraction reflection shell
Highest resolution (Å)Lowest resolution (Å)% possible obs (%)IDRmerge(I) obsChi squaredRedundancy
5.025098.810.0665.53122.1
3.995.0299.810.0543.18125.1
3.483.9999.910.0542.76225.8
3.163.4810010.0612.30426.1
2.943.1610010.0711.94826
2.762.9410010.0771.61425.8
2.632.7610010.091.36925.5
2.512.6310010.1021.25425.5
2.412.5110010.1221.16325.2
2.332.4110010.131.05725.1
2.262.3310010.1511.00425.1
2.192.2610010.170.95624.9
2.142.1910010.1920.91525
2.082.1410010.2330.84725.1
2.042.0810010.2850.81625
1.992.0410010.3240.7824.1
1.951.9910010.4180.7221.9
1.921.959910.5110.67319
1.881.9296.610.6580.65816.8
1.851.8894.610.7820.62815.4
ReflectionResolution: 1.85→50 Å / Num. all: 20449 / Num. obs: 20449 / % possible obs: 99.4 % / Observed criterion σ(I): -3 / Redundancy: 23.8 % / Biso Wilson estimate: 29.4 Å2 / Rmerge(I) obs: 0.074 / Χ2: 1.59 / Net I/σ(I): 9.9
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2% possible all
1.85-1.8815.40.7829170.62894.6
1.88-1.9216.80.6589650.65896.6
1.92-1.95190.51110160.67399
1.95-1.9921.90.4189840.72100
1.99-2.0424.10.32410060.78100
2.04-2.08250.2859970.816100
2.08-2.1425.10.23310140.847100
2.14-2.19250.19210080.915100
2.19-2.2624.90.1710090.956100
2.26-2.3325.10.15110141.004100
2.33-2.4125.10.1310071.057100
2.41-2.5125.20.12210161.163100
2.51-2.6325.50.10210191.254100
2.63-2.7625.50.0910261.369100
2.76-2.9425.80.07710371.614100
2.94-3.16260.07110301.948100
3.16-3.4826.10.06110462.304100
3.48-3.9925.80.05410592.76299.9
3.99-5.0225.10.05410943.18199.8
5.02-5022.10.06611855.53198.8

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Phasing

PhasingMethod: SAD
Phasing MADD res high: 1.9 Å / D res low: 50 Å / FOM : 0.3 / FOM acentric: 0.368 / FOM centric: 0 / Reflection: 19288 / Reflection acentric: 15730 / Reflection centric: 3558
Phasing MAD setR cullis acentric: 1.82 / R cullis centric: 1 / Highest resolution: 1.9 Å / Lowest resolution: 50 Å / Loc acentric: 0.1 / Loc centric: 0.1 / Power acentric: 0 / Power centric: 0 / Reflection acentric: 15730 / Reflection centric: 3558
Phasing MAD set shell

ID: 1 / R cullis centric: 1 / Power acentric: 0 / Power centric: 0

Resolution (Å)R cullis acentricLoc acentricLoc centricReflection acentricReflection centric
12.01-501.530.40.23069
6.82-12.011.640.30.2217181
4.76-6.821.570.30.1592290
3.66-4.761.080.20.21145393
2.97-3.661.340.10.11887498
2.5-2.972.360.102801613
2.16-2.53.010.103894718
1.9-2.164.76005164796
Phasing MAD set site

Atom type symbol: Se / Occupancy iso: 0

IDB isoFract xFract yFract zOccupancy
137.87330.1360.7650.0544.066
254.89320.0680.631-0.0363.432
3105.21410.0210.673-0.0853.171
Phasing MAD shell
Resolution (Å)FOM FOM acentricFOM centricReflectionReflection acentricReflection centric
12.01-500.1650.5440993069
6.82-12.010.3590.6580398217181
4.76-6.820.4050.6040882592290
3.66-4.760.4470.601015381145393
2.97-3.660.4480.566023851887498
2.5-2.970.3980.485034142801613
2.16-2.50.2930.347046123894718
1.9-2.160.1350.156059605164796
Phasing dmMethod: Solvent flattening and Histogram matching / Reflection: 20352
Phasing dm shell
Resolution (Å)Delta phi finalFOM Reflection
6.8-10073.40.753506
5.32-6.863.90.86504
4.61-5.3259.60.88511
4.16-4.6165.20.894509
3.84-4.1657.80.889524
3.59-3.8458.60.898541
3.38-3.5960.40.884579
3.2-3.3861.60.895608
3.05-3.260.80.892648
2.92-3.0559.10.88660
2.8-2.9264.50.886702
2.7-2.859.90.874722
2.6-2.760.30.883740
2.52-2.661.20.892756
2.44-2.5261.90.878799
2.38-2.4461.30.885815
2.31-2.3861.40.89835
2.25-2.3167.40.88849
2.2-2.25670.898856
2.15-2.2620.886894
2.1-2.1567.10.873909
2.05-2.169.70.869939
2.01-2.05720.884925
1.97-2.0175.90.862976
1.94-1.9776.90.844974
1.9-1.9476.80.808976
1.85-1.988.50.7511095

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
MLPHAREphasing
DM6.1phasing
REFMACrefinement
PDB_EXTRACT3.1data extraction
SBC-Collectdata collection
HKL-3000data reduction
HKL-3000data scaling
HKL-3000phasing
SHELXDphasing
SHELXEmodel building
SOLVEphasing
RESOLVEphasing
ARP/wARPmodel building
CCP4phasing
Omodel building
Cootmodel building
RefinementMethod to determine structure: SAD / Resolution: 1.86→34.43 Å / Cor.coef. Fo:Fc: 0.966 / Cor.coef. Fo:Fc free: 0.961 / WRfactor Rfree: 0.1871 / WRfactor Rwork: 0.166 / Occupancy max: 1 / Occupancy min: 0.3 / FOM work R set: 0.9098 / SU B: 4.157 / SU ML: 0.057 / SU R Cruickshank DPI: 0.0999 / SU Rfree: 0.0951 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.095
Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.1904 1034 5.1 %RANDOM
Rwork0.1703 ---
all0.1713 20287 --
obs0.1713 20287 98.47 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso max: 81.66 Å2 / Biso mean: 35.5082 Å2 / Biso min: 20.43 Å2
Baniso -1Baniso -2Baniso -3
1-1.25 Å20.63 Å20 Å2
2--1.25 Å20 Å2
3----1.88 Å2
Refinement stepCycle: LAST / Resolution: 1.86→34.43 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1068 0 55 160 1283
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0221192
X-RAY DIFFRACTIONr_bond_other_d0.0010.02854
X-RAY DIFFRACTIONr_angle_refined_deg1.3951.9691607
X-RAY DIFFRACTIONr_angle_other_deg0.8613.0032046
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.4895144
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.1923.87162
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.01115191
X-RAY DIFFRACTIONr_dihedral_angle_4_deg12.224158
X-RAY DIFFRACTIONr_chiral_restr0.0860.2172
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0211298
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02253
X-RAY DIFFRACTIONr_mcbond_it0.8091.5684
X-RAY DIFFRACTIONr_mcbond_other0.2211.5270
X-RAY DIFFRACTIONr_mcangle_it1.48421119
X-RAY DIFFRACTIONr_scbond_it2.3533508
X-RAY DIFFRACTIONr_scangle_it3.9474.5481
LS refinement shellResolution: 1.86→1.908 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.235 80 -
Rwork0.228 1231 -
all-1311 -
obs--88.28 %
Refinement TLS params.Method: refined / Origin x: 11.7707 Å / Origin y: 19.5791 Å / Origin z: -5.1925 Å
111213212223313233
T0.0809 Å2-0.018 Å20.0276 Å2-0.0191 Å20.0058 Å2--0.0259 Å2
L2.1761 °2-0.1526 °2-0.7847 °2-1.9064 °20.6892 °2--2.7434 °2
S-0.0751 Å °0.0301 Å °-0.0302 Å °0.2011 Å °0.0128 Å °0.0392 Å °-0.0232 Å °0.0482 Å °0.0623 Å °

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