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- PDB-4kwy: Crystal structure of a putative lipoprotein (CC_3750) from Caulob... -

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Basic information

Entry
Database: PDB / ID: 4kwy
TitleCrystal structure of a putative lipoprotein (CC_3750) from Caulobacter crescentus CB15 at 2.40 A resolution
ComponentsPutative uncharacterized protein
KeywordsTRANSPORT PROTEIN / LptE / PF04390 family / lipoprotein / Structural Genomics / Joint Center for Structural Genomics / JCSG / Protein Structure Initiative / PSI-BIOLOGY
Function / homology
Function and homology information


outer membrane / Gram-negative-bacterium-type cell outer membrane assembly
Similarity search - Function
Lipoprotein like domain / Lipopolysaccharide-assembly / LPS-assembly lipoprotein LptE / Double Stranded RNA Binding Domain / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
PHOSPHATE ION / Uncharacterized protein
Similarity search - Component
Biological speciesCaulobacter crescentus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.4 Å
AuthorsJoint Center for Structural Genomics (JCSG)
CitationJournal: To be published
Title: Crystal structure of a hypothetical protein (CC_3750) from Caulobacter crescentus CB15 at 2.40 A resolution (PSI Community Target, Shapiro)
Authors: Joint Center for Structural Genomics (JCSG)
History
DepositionMay 24, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 19, 2013Provider: repository / Type: Initial release
Revision 1.1Dec 24, 2014Group: Structure summary
Revision 1.2Nov 15, 2017Group: Refinement description / Category: software
Revision 1.3Jan 24, 2018Group: Database references / Category: citation_author / Item: _citation_author.name
Revision 1.4Feb 1, 2023Group: Database references / Derived calculations
Category: database_2 / pdbx_struct_special_symmetry ...database_2 / pdbx_struct_special_symmetry / 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Putative uncharacterized protein
B: Putative uncharacterized protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,6135
Polymers30,4482
Non-polymers1663
Water2,666148
1
A: Putative uncharacterized protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)15,2592
Polymers15,2241
Non-polymers351
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Putative uncharacterized protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)15,3543
Polymers15,2241
Non-polymers1302
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)88.442, 136.351, 60.211
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number20
Space group name H-MC2221
Components on special symmetry positions
IDModelComponents
11B-202-

PO4

21B-377-

HOH

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Components

#1: Protein Putative uncharacterized protein


Mass: 15223.759 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Caulobacter crescentus (bacteria) / Strain: CB15 / Gene: CC_3750 / Plasmid: SpeedET / Production host: Escherichia Coli (E. coli) / Strain (production host): PB1 / References: UniProt: Q9A216
#2: Chemical ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#3: Chemical ChemComp-PO4 / PHOSPHATE ION / Phosphate


Mass: 94.971 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: PO4
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 148 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsTHE CONSTRUCT (28-166) WAS EXPRESSED WITH A PURIFICATION TAG MGSDKIHHHHHHENLYFQG. THE TAG WAS ...THE CONSTRUCT (28-166) 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: 2.98 Å3/Da / Density % sol: 58.74 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop
Details: 0.17M potassium dihydrogen phosphate, 20% polyethylene glycol 3350, 0.01M trimethylamine HCl, NANODROP, VAPOR DIFFUSION, SITTING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL11-1 / Wavelength: 0.97805, 0.91837, 0.97871
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: May 2, 2013
Details: Flat mirror (vertical focusing); single crystal Si(111) bent monochromator (horizontal focusing)
RadiationMonochromator: single crystal Si(111) bent / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.978051
20.918371
30.978711
ReflectionResolution: 2.4→46.754 Å / Num. obs: 14362 / % possible obs: 98.1 % / Observed criterion σ(I): -3 / Biso Wilson estimate: 53.25 Å2 / Rmerge(I) obs: 0.095 / Net I/σ(I): 12.2
Reflection shell

Diffraction-ID: 1

Resolution (Å)Highest resolution (Å)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. unique obs% possible all
2.4-2.460.9081.84965105698.8
2.46-2.530.7782.24701102098.6
2.53-2.60.5522.8443798598.9
2.6-2.680.4933.3406493195.6
2.68-2.770.394.2431492798
2.77-2.870.3035.4440792599.4
2.87-2.980.2346.8424188899.2
2.98-3.10.1788.4392883998.8
3.1-3.240.1311.2383782399
3.24-3.390.09713.6356678999.1
3.39-3.580.0717.7300468792.7
3.58-3.790.06420.7339671299.3
3.79-4.060.05521.8319068399.6
4.06-4.380.05124.4290761699.2
4.38-4.80.04925.3259058098.5
4.8-5.370.05125211950093.8
5.37-6.20.05524.2215247099.4
6.2-7.590.04626.9178340599.3
7.59-10.730.03731.2124229992.6
10.730.02737.279819898.5

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Phasing

PhasingMethod: MAD

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Processing

Software
NameVersionClassificationNB
MolProbity3beta29model building
PDB_EXTRACT3.1data extraction
SHELXphasing
SHARPphasing
XSCALEJuly 4, 2012data scaling
BUSTER-TNT2.10.0refinement
XDSdata reduction
SHELXDphasing
BUSTER2.10.0refinement
RefinementMethod to determine structure: MAD / Resolution: 2.4→46.754 Å / Cor.coef. Fo:Fc: 0.9378 / Cor.coef. Fo:Fc free: 0.9192 / Occupancy max: 1 / Occupancy min: 0.5 / 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. ATOM RECORD CONTAINS SUM OF TLS AND RESIDUAL B FACTORS. ANISOU RECORD CONTAINS SUM OF TLS AND RESIDUAL U FACTORS. 3. NCS RESTRAINTS WERE IMPOSED BY AUTOBUSTER'S LSSR PROCEDURE (-AUTONCS). 4. CHLORIDE (CL) AND PHOSPHATE (PO4) MODELED WERE PRESENT IN PROTEIN BUFFER / CRYSTALLIZATION CONDITIONS. 5. THE MAD PHASES WERE USED AS RESTRAINTS DURING REFINEMENT. 6. THE MODEL FOR RESIDUES 87-90 OF CHAIN B, LOCATED NEAR OR ON THE TWO-FOLD AXIS, WAS NOT BUILT DUE TO DIFFICULTY IN MODELING THE ALTERNATIVE CONFORMATIONS FOR THIS REGION.
RfactorNum. reflection% reflectionSelection details
Rfree0.2412 721 5.02 %RANDOM
Rwork0.1917 ---
obs0.1942 14352 98.13 %-
Displacement parametersBiso max: 165.12 Å2 / Biso mean: 56.6743 Å2 / Biso min: 22.2 Å2
Baniso -1Baniso -2Baniso -3
1--0.0911 Å20 Å20 Å2
2---1.8872 Å20 Å2
3---1.9783 Å2
Refine analyzeLuzzati coordinate error obs: 0.351 Å
Refinement stepCycle: LAST / Resolution: 2.4→46.754 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2043 0 7 148 2198
Refine LS restraints
Refine-IDTypeNumberRestraint functionWeightDev ideal
X-RAY DIFFRACTIONt_dihedral_angle_d976SINUSOIDAL2
X-RAY DIFFRACTIONt_trig_c_planes60HARMONIC2
X-RAY DIFFRACTIONt_gen_planes311HARMONIC5
X-RAY DIFFRACTIONt_it2075HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_chiral_improper_torsion260SEMIHARMONIC5
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_contact2347SEMIHARMONIC4
X-RAY DIFFRACTIONt_bond_d2075HARMONIC20.01
X-RAY DIFFRACTIONt_angle_deg2803HARMONIC21.06
X-RAY DIFFRACTIONt_omega_torsion3.18
X-RAY DIFFRACTIONt_other_torsion2.98
LS refinement shellResolution: 2.4→2.59 Å / Total num. of bins used: 7
RfactorNum. reflection% reflection
Rfree0.2765 150 5.13 %
Rwork0.2188 2774 -
all0.2218 2924 -
obs--98.13 %
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)
11.86612.91042.51525.02352.91044.84780.1163-0.2020.280.1937-0.04840.09890.24260.1237-0.0679-0.1749-0.0078-0.0225-0.0826-0.152-0.158415.451732.148536.7429
24.73991.3954-0.3732.4602-0.10221.87730.1349-0.4479-0.37740.2324-0.1936-0.31690.24480.14150.0587-0.0049-0.0256-0.0547-0.13550.0726-0.116111.341911.655825.781
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1{A|30 - 166}A30 - 166
2X-RAY DIFFRACTION2{B|28 - 163}B28 - 163

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