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- PDB-5cai: Crystal structure of a putative lipoprotein from the DUF903 famil... -

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Basic information

Entry
Database: PDB / ID: 5cai
TitleCrystal structure of a putative lipoprotein from the DUF903 family (KPN_03160) from Klebsiella pneumoniae subsp. pneumoniae MGH 78578 at 2.30 A resolution
ComponentsPutative lipoprotein from the DUF903 family
KeywordsLIPID BINDING PROTEIN / lipoprotein / Structural Genomics / Joint Center for Structural Genomics / JCSG / Protein Structure Initiative / PSI-BIOLOGY / LIPID-BINDING PROTEIN
Function / homology
Function and homology information


Protein of unknown function DUF903 / : / Bacterial protein of unknown function (DUF903) / SH3 type barrels. - #100 / LSM domain superfamily / SH3 type barrels. / Prokaryotic membrane lipoprotein lipid attachment site profile. / Roll / Mainly Beta
Similarity search - Domain/homology
Lipoprotein YgdI/YgdR-like SH3-like domain-containing protein
Similarity search - Component
Biological speciesKlebsiella pneumoniae subsp. pneumoniae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.3 Å
AuthorsJoint Center for Structural Genomics (JCSG)
CitationJournal: To be published
Title: Crystal structure of a putative lipoprotein from the DUF903 family (KPN_03160) from Klebsiella pneumoniae subsp. pneumoniae MGH 78578 at 2.30 A resolution
Authors: Joint Center for Structural Genomics (JCSG)
History
DepositionJun 29, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 22, 2015Provider: repository / Type: Initial release
Revision 1.1Jan 24, 2018Group: Database references / Derived calculations ...Database references / Derived calculations / Source and taxonomy / Structure summary
Category: citation_author / entity_src_gen ...citation_author / entity_src_gen / pdbx_struct_oper_list / struct_keywords
Item: _citation_author.name / _entity_src_gen.pdbx_alt_source_flag ..._citation_author.name / _entity_src_gen.pdbx_alt_source_flag / _pdbx_struct_oper_list.symmetry_operation / _struct_keywords.pdbx_keywords / _struct_keywords.text
Revision 1.2Feb 1, 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
Revision 1.3Oct 23, 2024Group: Data collection / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_entry_details / pdbx_modification_feature
Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Putative lipoprotein from the DUF903 family
B: Putative lipoprotein from the DUF903 family
C: Putative lipoprotein from the DUF903 family
D: Putative lipoprotein from the DUF903 family
E: Putative lipoprotein from the DUF903 family
F: Putative lipoprotein from the DUF903 family
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,32015
Polymers38,0016
Non-polymers3199
Water4,306239
1
A: Putative lipoprotein from the DUF903 family
B: Putative lipoprotein from the DUF903 family
E: Putative lipoprotein from the DUF903 family
hetero molecules

A: Putative lipoprotein from the DUF903 family
B: Putative lipoprotein from the DUF903 family
E: Putative lipoprotein from the DUF903 family
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,35616
Polymers38,0016
Non-polymers35510
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation10_555-x,-y,z1
2
C: Putative lipoprotein from the DUF903 family
D: Putative lipoprotein from the DUF903 family
F: Putative lipoprotein from the DUF903 family
hetero molecules

C: Putative lipoprotein from the DUF903 family
D: Putative lipoprotein from the DUF903 family
F: Putative lipoprotein from the DUF903 family
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,28514
Polymers38,0016
Non-polymers2848
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation10_555-x,-y,z1
Unit cell
Length a, b, c (Å)108.210, 108.210, 142.190
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number98
Space group name H-MI4122
Components on special symmetry positions
IDModelComponents
11E-247-

HOH

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Components

#1: Protein
Putative lipoprotein from the DUF903 family


Mass: 6333.536 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Klebsiella pneumoniae subsp. pneumoniae (bacteria)
Strain: ATCC 700721 / MGH 78578 / Gene: ygdI, YP_001336791.1 / Plasmid: SpeedET / Production host: Escherichia Coli (E. coli) / Strain (production host): PB1 / References: UniProt: A6TD90
#2: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: Cl
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 239 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY
Sequence detailsTHE CONSTRUCT (22-76) WAS EXPRESSED WITH A PURIFICATION TAG MGSDKIHHHHHHENLYFQG. THE TAG WAS ...THE CONSTRUCT (22-76) WAS EXPRESSED WITH A PURIFICATION TAG MGSDKIHHHHHHENLYFQG. THE TAG WAS REMOVED WITH TEV PROTEASE LEAVING ONLY A GLYCINE (0) FOLLOWED BY THE TARGET SEQUENCE.

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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: 2.74 Å3/Da / Density % sol: 55.08 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop
Details: 0.2M di-ammonium tartrate, 20.0% polyethylene glycol 3350, 0.2M di-ammonium tartrate, 20.0% polyethylene glycol 3350

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL14-1 / Wavelength: 0.95369,0.97934,0.97919
DetectorType: MARMOSAIC 325 mm CCD / Detector: CCD / Date: Apr 12, 2015
Details: Vertical focusing mirror; double crystal Si(111) monochromator
RadiationMonochromator: double crystal Si(111) / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.953691
20.979341
30.979191
ReflectionResolution: 2.3→29.709 Å / Num. all: 19120 / Num. obs: 19120 / % possible obs: 99.9 % / Redundancy: 7.3 % / Rpim(I) all: 0.06 / Rrim(I) all: 0.163 / Rsym value: 0.151 / Net I/av σ(I): 4.872 / Net I/σ(I): 10.3 / Num. measured all: 139561
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) allRmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allRpim(I) allRrim(I) allRsym valueDiffraction-IDNet I/σ(I) obs% possible all
2.3-2.367.40.9680.9010.91031913970.3530.9680.90112.399.9
2.36-2.427.40.7090.6591.2997713430.2580.7090.6593.1100
2.42-2.497.40.6680.6211.2971613180.2440.6680.6213.3100
2.49-2.577.40.5730.5321.4950812860.2090.5730.5323.8100
2.57-2.667.40.5360.4991.5908412300.1950.5360.4994.1100
2.66-2.757.40.4860.4521.7905712220.1770.4860.4524.4100
2.75-2.857.30.3870.362.1848811560.1410.3870.365.4100
2.85-2.977.40.2840.2642.9824711180.1040.2840.2647.2100
2.97-3.17.30.2350.2183.5798210900.0860.2350.2188.4100
3.1-3.257.40.1740.1624.7767610380.0640.1740.16210.8100
3.25-3.437.30.1330.123671469780.0490.1330.12314.3100
3.43-3.647.30.1290.126.268739390.0470.1290.1215.1100
3.64-3.897.30.10.093864358850.0370.10.09318.3100
3.89-4.27.30.0760.07110.360008240.0280.0760.07121.8100
4.2-4.67.20.0660.06111.355017610.0240.0660.06124.2100
4.6-5.147.20.0590.05512.550417030.0220.0590.05525.6100
5.14-5.947.10.0920.085843706180.0340.0920.08518.6100
5.94-7.2770.0930.0867.837385340.0340.0930.08617.5100
7.27-10.296.70.0760.0719.529074320.0290.0760.07120.1100
10.29-29.70960.0460.04112.714962480.0190.0460.04124.295.9

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Phasing

PhasingMethod: MAD

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Processing

Software
NameVersionClassification
PDB_EXTRACT3.1data extraction
MOSFLMdata reduction
SCALA3.3.20data scaling
SHELXphasing
SHARPphasing
SHELXDphasing
BUSTER2.10.2refinement
RefinementMethod to determine structure: MAD / Resolution: 2.3→29.709 Å / Cor.coef. Fo:Fc: 0.9441 / Cor.coef. Fo:Fc free: 0.9248 / Occupancy max: 1 / Occupancy min: 0.37 / Cross valid method: THROUGHOUT / σ(F): 0
Details: 1. 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 FOR THE REDUCED ...Details: 1. 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 FOR THE REDUCED SCATTERING POWER DUE TO PARTIAL S-MET INCORPORATION. 2. THE MAD PHASES WERE USED AS RESTRAINTS DURING REFINEMENT. 3. HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. 4. ATOM RECORDS CONTAIN SUM OF TLS AND RESIDUAL B FACTORS. ANISOU RECORDS CONTAIN SUM OF TLS AND RESIDUAL U FACTORS.
RfactorNum. reflection% reflectionSelection details
Rfree0.2152 984 5.15 %RANDOM
Rwork0.1806 ---
obs0.1824 19104 99.99 %-
Displacement parametersBiso max: 132.37 Å2 / Biso mean: 41.2537 Å2 / Biso min: 11.83 Å2
Baniso -1Baniso -2Baniso -3
1-1.1349 Å20 Å20 Å2
2--1.1349 Å20 Å2
3----2.2698 Å2
Refine analyzeLuzzati coordinate error obs: 0.277 Å
Refinement stepCycle: LAST / Resolution: 2.3→29.709 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2466 0 9 239 2714
Refine LS restraints
Refine-IDTypeNumberRestraint functionWeightDev ideal
X-RAY DIFFRACTIONt_dihedral_angle_d1323SINUSOIDAL2
X-RAY DIFFRACTIONt_trig_c_planes108HARMONIC2
X-RAY DIFFRACTIONt_gen_planes399HARMONIC5
X-RAY DIFFRACTIONt_it2673HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_chiral_improper_torsion360SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact3014SEMIHARMONIC4
X-RAY DIFFRACTIONt_bond_d2673HARMONIC20.01
X-RAY DIFFRACTIONt_angle_deg3645HARMONIC21.1
X-RAY DIFFRACTIONt_omega_torsion2.81
X-RAY DIFFRACTIONt_other_torsion2.75
LS refinement shellResolution: 2.3→2.42 Å / Total num. of bins used: 10
RfactorNum. reflection% reflection
Rfree0.2346 138 5.04 %
Rwork0.1948 2598 -
all0.1968 2736 -
obs--99.99 %
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)
14.7975-2.8361-0.69354.0108-0.29787.14620.03620.24880.2766-0.3228-0.1904-0.54420.02260.46290.1542-0.11960.01760.1083-0.10650.07460.053917.01318.044722.6202
24.51851.2477-0.26895.62690.7874.005-0.11260.3063-0.3296-0.40650.0774-0.45160.13210.40650.0352-0.05190.04840.0897-0.0910.0114-0.020915.8455-10.971122.1722
32.5317-1.9498-0.13846.21190.13484.0102-0.0885-0.21940.42040.46280.1098-0.5442-0.22540.3138-0.0213-0.0952-0.0427-0.0922-0.0761-0.06190.026813.607213.339348.3273
46.75642.6791.78834.47031.11614.21030.0687-0.28720.03390.2347-0.078-0.54420.18580.41920.0093-0.1097-0.0128-0.0824-0.07040.04240.001718.4576-5.02448.1953
52.7002-0.4067-0.20482.919-0.25872.95680.10930.13970.3834-0.2676-0.166-0.2289-0.31290.0810.0567-0.0184-0.00150.0243-0.08520.05990.02131.192518.742822.3398
63.30850.0483-0.00152.97370.52363.2042-0.0410.01940.54380.26660.02020.1943-0.2733-0.16230.0207-0.05120.0194-0.0161-0.0882-0.03980.0285-4.94918.742947.3281
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1{A|23 - 75}A23 - 75
2X-RAY DIFFRACTION2{B|23 - 75}B23 - 75
3X-RAY DIFFRACTION3{C|24 - 75}C24 - 75
4X-RAY DIFFRACTION4{D|23 - 75}D23 - 75
5X-RAY DIFFRACTION5{E|24 - 75}E24 - 75
6X-RAY DIFFRACTION6{F|23 - 75}F23 - 75

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