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- PDB-4pwt: Crystal structure of peptidoglycan-associated outer membrane lipo... -

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Basic information

Entry
Database: PDB / ID: 4pwt
TitleCrystal structure of peptidoglycan-associated outer membrane lipoprotein from Yersinia pestis CO92
ComponentsPeptidoglycan-associated lipoprotein
KeywordsMEMBRANE PROTEIN / peptidoglycan-associated outer membrane lipoprotein / alpha-beta fold / Structural Genomics / NIAID / National Institute of Allergy and Infectious Diseases / Center for Structural Genomics of Infectious Diseases / CSGID
Function / homology
Function and homology information


cell outer membrane / cell cycle / cell division
Similarity search - Function
Peptidoglycan-associated lipoprotein, C-terminal / Peptidoglycan-associated lipoprotein / Outer membrane protein, OmpA-like, conserved site / OmpA-like domain. / OmpA-like domain / Outer membrane protein, bacterial / OmpA-like domain superfamily / OmpA family / OmpA-like domain / OmpA-like domain profile. ...Peptidoglycan-associated lipoprotein, C-terminal / Peptidoglycan-associated lipoprotein / Outer membrane protein, OmpA-like, conserved site / OmpA-like domain. / OmpA-like domain / Outer membrane protein, bacterial / OmpA-like domain superfamily / OmpA family / OmpA-like domain / OmpA-like domain profile. / 60s Ribosomal Protein L30; Chain: A; / Prokaryotic membrane lipoprotein lipid attachment site profile. / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
FORMIC ACID / PYROPHOSPHATE 2- / Peptidoglycan-associated lipoprotein / Peptidoglycan-associated lipoprotein
Similarity search - Component
Biological speciesYersinia pestis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.752 Å
AuthorsMaltseva, N. / Kim, Y. / Osipiuk, J. / Anderson, W.F. / Joachimiak, A. / Center for Structural Genomics of Infectious Diseases (CSGID)
CitationJournal: To be Published
Title: Crystal structure of peptidoglycan-associated outer membrane lipoprotein from Yersinia pestis CO92
Authors: Maltseva, N. / Kim, Y. / Osipiuk, J. / Anderson, W.F. / Joachimiak, A.
History
DepositionMar 21, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 9, 2014Provider: repository / Type: Initial release
Revision 1.1Sep 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / 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 1.2Dec 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

Downloads & links

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Assembly

Deposited unit
A: Peptidoglycan-associated lipoprotein
B: Peptidoglycan-associated lipoprotein
C: Peptidoglycan-associated lipoprotein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)44,1758
Polymers43,7153
Non-polymers4605
Water4,306239
1
A: Peptidoglycan-associated lipoprotein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,7643
Polymers14,5721
Non-polymers1922
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Peptidoglycan-associated lipoprotein


Theoretical massNumber of molelcules
Total (without water)14,5721
Polymers14,5721
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: Peptidoglycan-associated lipoprotein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,8404
Polymers14,5721
Non-polymers2683
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)65.015, 65.015, 86.967
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number144
Space group name H-MP31

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Components

#1: Protein Peptidoglycan-associated lipoprotein / Peptidoglycan-associated lipoprotein Pal


Mass: 14571.688 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Yersinia pestis (bacteria) / Strain: CO92 / Gene: excC, pal, y3054, YPO1125, YP_1031 / Plasmid: pMCSG68 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21magic / References: UniProt: Q7CH55, UniProt: A0A380PP88*PLUS
#2: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-FMT / FORMIC ACID / Formic acid


Mass: 46.025 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: CH2O2
#4: Chemical ChemComp-POP / PYROPHOSPHATE 2- / Pyrophosphate


Mass: 175.959 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: H2O7P2
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 239 / 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: 2.43 Å3/Da / Density % sol: 49.33 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 5.5
Details: 0.2M lithium sulfate, 0.1M Bis-Tris pH 5.5, 25% PEG 3350, 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: 0.97926 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Nov 17, 2013 / Details: mirrors
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97926 Å / Relative weight: 1
ReflectionResolution: 1.75→50 Å / Num. all: 41239 / Num. obs: 41239 / % possible obs: 99.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4.1 % / Biso Wilson estimate: 18.83 Å2 / Rsym value: 0.053 / Net I/σ(I): 12
Reflection shellResolution: 1.75→1.79 Å / Redundancy: 4.1 % / Mean I/σ(I) obs: 2.6 / Num. unique all: 2046 / Rsym value: 0.727 / % possible all: 100

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Processing

Software
NameVersionClassification
SBC-Collectdata collection
HKL-3000data collection
HKL-3000phasing
MOLREPphasing
ARP/wARPmodel building
PHENIX(phenix.refine: dev_1593)refinement
HKL-3000data reduction
HKL-3000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1OAP

1oap


Resolution: 1.752→26.784 Å / SU ML: 0.18 / Isotropic thermal model: mixed / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Phase error: 19.9 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2 2076 5.05 %random
Rwork0.168 ---
all0.17 41114 --
obs0.17 41114 99.59 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 25.3 Å2
Refinement stepCycle: LAST / Resolution: 1.752→26.784 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2977 0 25 239 3241
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0073358
X-RAY DIFFRACTIONf_angle_d1.064563
X-RAY DIFFRACTIONf_dihedral_angle_d15.6391281
X-RAY DIFFRACTIONf_chiral_restr0.074473
X-RAY DIFFRACTIONf_plane_restr0.004628
LS refinement shell

Refine-ID: X-RAY DIFFRACTION

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection obs% reflection obs (%)
1.7521-1.79280.2351550.20012466262197
1.7928-1.83760.25881310.198226272758100
1.8376-1.88730.26231450.20625822727100
1.8873-1.94280.23821420.203425912733100
1.9428-2.00550.28091300.186326802810100
2.0055-2.07720.21331110.180826042715100
2.0772-2.16030.22191360.17726512787100
2.1603-2.25860.21621340.165526212755100
2.2586-2.37760.1971280.165626002728100
2.3776-2.52640.21721560.173426132768100
2.5264-2.72130.23911370.176926312768100
2.7213-2.99490.20461580.185425782736100
2.9949-3.42750.19811410.172726152756100
3.4275-4.31530.1621510.137926262777100
4.3153-26.78710.14731210.14532553267498
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)
15.42842.126-0.19465.111-0.74093.5904-0.00660.10551.2291-0.00250.24230.0884-0.1955-0.68320.0530.2523-0.07940.02110.44750.0060.3366-19.99141.854813.5368
26.96371.6260.93752.2724-0.19882.9963-0.11890.154-0.609-0.09730.0888-0.45240.7711-0.4974-0.02460.3327-0.1735-0.01720.38010.01550.0704-14.016333.790317.9878
36.1120.09160.51241.4904-0.87782.35-0.05550.07370.76080.0395-0.0030.0019-0.12490.09870.0370.120.04340.01910.147-0.0130.129-4.291135.343632.5109
48.1829-1.8039-0.15671.5957-0.5021.8398-0.04630.1407-0.2580.01140.05170.04860.33460.3827-0.02160.14090.07510.00890.2052-0.01350.1130.31326.003933.59
52.0838-1.9243-1.03462.82370.32352.06350.08110.3693-0.2318-0.1114-0.1376-0.15980.29790.28570.11720.18030.09490.00070.26390.00570.10422.110525.269128.1345
66.88853.99191.61746.13520.39483.7127-0.08660.48520.321-0.2248-0.1292-0.31390.01030.51430.18110.150.05570.03210.31580.02520.14645.713132.422627.3165
70.63391.70621.69614.64644.50094.485-0.06180.52980.537-0.287-0.0784-0.5056-0.4110.18320.2030.17290.0149-0.02830.27110.01440.4174-12.016455.408845.223
86.2131-0.1826.00660.9718-0.92416.32250.1199-0.03970.12260.0451-0.0679-0.13660.30050.12220.05110.14990.0387-0.01430.1753-0.02920.1633-21.903150.81738.2122
95.4349-0.39681.8140.644-0.00411.7232-0.22390.07410.5346-0.0490.0856-0.1091-0.16330.19940.13410.1228-0.0148-0.00920.15590.01990.2022-27.593451.545126.1555
107.4579-0.81381.70730.7506-0.11652.08170.00710.075-0.2113-0.05680.03360.02910.01390.0869-0.0560.1130.0037-0.00390.09620.02050.1204-35.242645.495823.4842
116.098-2.0964-0.1147.8439-0.1833.3285-0.2588-1.01140.40310.52390.06440.5545-0.3481-0.36820.04170.19120.0746-0.01170.4029-0.04940.2552-46.416153.781232.185
122.4276-3.5212.04426.0031-1.75963.8851-0.1909-0.47130.0790.16210.08520.0683-0.1236-0.23420.28580.11290.031-0.03220.19010.03190.1586-33.920150.440231.1049
135.46162.6828-0.62566.39950.34348.10090.5616-0.2604-0.37221.37-0.3039-0.45710.9449-0.0689-0.22270.40990.0087-0.10130.27930.00450.2064-30.18651.647935.4096
141.52281.33450.62565.17551.09832.20630.0641-0.0722-0.058-0.0012-0.06350.08830.2495-0.12350.01520.1427-0.00030.01530.08990.0160.0966-23.665616.369150.2076
154.4877-0.4999-0.27246.5081-0.2283.9343-0.09030.13420.3299-0.1520.0915-0.0695-0.32630.1535-0.00550.1402-0.005-0.0130.11450.01250.106-22.104928.128843.7132
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid -1 through 48 )
2X-RAY DIFFRACTION2chain 'A' and (resid 49 through 62 )
3X-RAY DIFFRACTION3chain 'A' and (resid 63 through 92 )
4X-RAY DIFFRACTION4chain 'A' and (resid 93 through 131 )
5X-RAY DIFFRACTION5chain 'A' and (resid 132 through 154 )
6X-RAY DIFFRACTION6chain 'A' and (resid 155 through 168 )
7X-RAY DIFFRACTION7chain 'B' and (resid -1 through 48 )
8X-RAY DIFFRACTION8chain 'B' and (resid 49 through 67 )
9X-RAY DIFFRACTION9chain 'B' and (resid 68 through 102 )
10X-RAY DIFFRACTION10chain 'B' and (resid 103 through 142 )
11X-RAY DIFFRACTION11chain 'B' and (resid 143 through 161 )
12X-RAY DIFFRACTION12chain 'B' and (resid 162 through 168 )
13X-RAY DIFFRACTION13chain 'C' and (resid 46 through 60 )
14X-RAY DIFFRACTION14chain 'C' and (resid 61 through 144 )
15X-RAY DIFFRACTION15chain 'C' and (resid 145 through 168 )

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