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- PDB-3tv9: Crystal Structure of Putative Peptide Maturation Protein from Shi... -

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Basic information

Entry
Database: PDB / ID: 3tv9
TitleCrystal Structure of Putative Peptide Maturation Protein from Shigella flexneri
ComponentsPutative peptide maturation protein
KeywordsPEPTIDE BINDING PROTEIN / Structural Genomics / Center for Structural Genomics of Infectious Diseases / CSGID / alpha-beta / cytosol
Function / homology
Function and homology information


metallopeptidase activity
Similarity search - Function
PmbA/TldD fold / PmbA/TldD superfamily / Metalloprotease TldD/E, N-terminal domain / Metalloprotease TldD/PmbA, N-terminal / Metalloprotease TldD/PmbA superfamily / PmbA/TldA metallopeptidase domain 1 / PmbA/TldA metallopeptidase central domain / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Putative peptide maturation protein / Putative peptide maturation protein
Similarity search - Component
Biological speciesShigella flexneri (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.497 Å
AuthorsKim, Y. / Maltseva, N. / Gu, M. / Anderson, W.F. / Joachimiak, A. / Center for Structural Genomics of Infectious Diseases (CSGID)
CitationJournal: To be Published
Title: Crystal Structure of Putative Peptide Maturation Protein from
Authors: Kim, Y. / Maltseva, N. / Gu, M. / Anderson, W.F. / Joachimiak, A.
History
DepositionSep 19, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 5, 2011Provider: repository / Type: Initial release
Revision 1.1Dec 28, 2016Group: Database references

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Putative peptide maturation protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)50,4086
Polymers49,9351
Non-polymers4725
Water1,44180
1
A: Putative peptide maturation protein
hetero molecules

A: Putative peptide maturation protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)100,81512
Polymers99,8712
Non-polymers94510
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_665-x+1,-y+1,z1
Buried area5720 Å2
ΔGint-77 kcal/mol
Surface area35900 Å2
MethodPISA
Unit cell
Length a, b, c (Å)115.133, 61.120, 65.101
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212
Components on special symmetry positions
IDModelComponents
11A-462-

HOH

Detailsdimer is generated by x,y,z and -x+1,-y+1,z

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Components

#1: Protein Putative peptide maturation protein


Mass: 49935.348 Da / Num. of mol.: 1 / Fragment: UNP residues 15-447
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Shigella flexneri (bacteria) / Strain: 2457T / Gene: pmbA, S4517 / Plasmid: pMCSG7 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) magic / References: UniProt: Q7UAN7, UniProt: A0A0H2W186*PLUS
#2: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 80 / 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: 2.29 Å3/Da / Density % sol: 46.37 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 0.1 M BIS-TRIS pH 6.5, 2.0 M Ammonium sulfate, 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: 0.97937 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Oct 31, 2010 / Details: mirrors
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97937 Å / Relative weight: 1
ReflectionResolution: 2.5→50 Å / Num. all: 16534 / Num. obs: 16534 / % possible obs: 99.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 6.2 % / Biso Wilson estimate: 39.75 Å2 / Rsym value: 0.096 / Net I/σ(I): 9
Reflection shellResolution: 2.5→2.54 Å / Redundancy: 6.4 % / Mean I/σ(I) obs: 3.62 / Num. unique all: 801 / Rsym value: 0.569 / % possible all: 100

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Processing

Software
NameVersionClassification
SBC-Collectdata collection
HKL-3000data collection
HKL-3000phasing
PHENIXmodel building
PHENIX(phenix.refine: dev_851)refinement
HKL-3000data reduction
HKL-3000data scaling
PHENIXphasing
RefinementMethod to determine structure: SAD / Resolution: 2.497→43.125 Å / SU ML: 0.68 / Isotropic thermal model: mixed / Cross valid method: THROUGHOUT / σ(F): 0 / Phase error: 25.63 / Stereochemistry target values: MLHL
RfactorNum. reflection% reflectionSelection details
Rfree0.249 1592 9.92 %random
Rwork0.19 ---
all0.196 16043 --
obs0.196 16043 96.89 %-
Solvent computationShrinkage radii: 0.73 Å / VDW probe radii: 1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 46.096 Å2 / ksol: 0.389 e/Å3
Displacement parametersBiso mean: 45.5 Å2
Baniso -1Baniso -2Baniso -3
1-9.6549 Å2-0 Å20 Å2
2---9.0375 Å2-0 Å2
3----0.6175 Å2
Refinement stepCycle: LAST / Resolution: 2.497→43.125 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3306 0 27 80 3413
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0093398
X-RAY DIFFRACTIONf_angle_d1.2264600
X-RAY DIFFRACTIONf_dihedral_angle_d15.4251229
X-RAY DIFFRACTIONf_chiral_restr0.096517
X-RAY DIFFRACTIONf_plane_restr0.007596
LS refinement shell

Refine-ID: X-RAY DIFFRACTION

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection obs% reflection obs (%)
2.4969-2.57740.35691220.25221205132791
2.5774-2.66960.32211450.23261248135394
2.6696-2.77640.3381300.22911282141295
2.7764-2.90280.31161470.22291267141496
2.9028-3.05580.27371440.22711299144397
3.0558-3.24720.29211420.20761296143897
3.2472-3.49780.2641480.19331327147599
3.4978-3.84960.19171620.16351343150599
3.8496-4.40610.19041410.13771348148999
4.4061-5.54940.20161490.155913831532100
5.5494-43.1310.27621620.21421453161599
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)
11.2826-1.0965-0.07064.38882.40014.7652-0.1912-0.0894-0.12040.25420.0337-0.13040.1985-0.20760.22250.20190.02210.04510.2540.03780.229447.778333.800932.0144
21.6284-0.61960.40584.37920.79861.6944-0.0613-0.06730.0379-0.02440.0949-0.3716-0.08150.0668-0.03450.29160.0225-0.00090.1916-0.01670.230454.750339.610525.9854
31.5421-0.8291-0.74364.4511.4481.9036-0.0287-0.0186-0.16260.2606-0.02480.04780.5368-0.1087-0.05580.2394-0.0133-0.09220.23850.03340.244943.811516.303614.7606
41.3384-0.9528-0.33715.1774.12573.43340.11250.033-0.0022-0.1232-0.23210.0205-0.1667-0.20520.02450.37950.01680.01430.26190.05750.207644.485526.140820.4877
52.2671-0.72390.07252.48260.94466.80080.10930.0128-0.0651-0.3619-0.1505-0.01250.27460.21640.0250.3529-0.00760.04680.1915-0.00570.310446.116613.42832.2758
60.5998-0.0203-0.74832.19460.74764.2124-0.0706-0.0264-0.0002-0.1577-0.0186-0.1252-0.01150.27130.06520.17260.0164-0.02740.19690.03840.216539.185436.9409-0.3034
70.97630.6770.71353.04930.47772.8231-0.01720.1048-0.0110.07390.090.05620.0656-0.0542-0.00340.18840.0421-0.00760.23080.02820.241634.013739.17715.6117
81.2963-1.7839-0.41994.88781.46775.5066-0.1811-0.0031-0.0424-0.30250.4174-1.19550.05880.5947-0.20070.2924-0.02620.05850.3322-0.03790.259547.322430.9662-10.0149
91.608-1.61-1.95653.63760.82572.97720.23690.12950.1021-0.2067-0.1032-0.4-0.25490.1713-0.1190.3537-0.03820.02670.31750.02420.271639.78729.8747-9.5985
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resseq 10:50)
2X-RAY DIFFRACTION2chain 'A' and (resseq 51:113)
3X-RAY DIFFRACTION3chain 'A' and (resseq 114:159)
4X-RAY DIFFRACTION4chain 'A' and (resseq 160:195)
5X-RAY DIFFRACTION5chain 'A' and (resseq 196:233)
6X-RAY DIFFRACTION6chain 'A' and (resseq 234:308)
7X-RAY DIFFRACTION7chain 'A' and (resseq 309:368)
8X-RAY DIFFRACTION8chain 'A' and (resseq 369:398)
9X-RAY DIFFRACTION9chain 'A' and (resseq 399:447)

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