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- PDB-4goq: Crystal structure of a DUF1491 family protein (CC_1065) from Caul... -

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Basic information

Entry
Database: PDB / ID: 4goq
TitleCrystal structure of a DUF1491 family protein (CC_1065) from Caulobacter crescentus CB15 at 1.87 A resolution
Componentshypothetical protein
KeywordsSTRUCTURAL GENOMICS / UNKNOWN FUNCTION / PF07372 family protein / DUF1491 / Joint Center for Structural Genomics / JCSG / Protein Structure Initiative / PSI-BIOLOGY
Function / homologyProtein of unknown function (DUF1491) / Protein of unknown function DUF1491 / Protein of unknown function (DUF1491) / hypothetical protein tt1805 / 3-Layer(aba) Sandwich / Alpha Beta / DUF1491 domain-containing protein
Function and homology information
Biological speciesCaulobacter crescentus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.87 Å
AuthorsJoint Center for Structural Genomics (JCSG)
CitationJournal: To be published
Title: Crystal structure of a hypothetical protein (CC_1065) from Caulobacter crescentus CB15 at 1.87 A resolution
Authors: Joint Center for Structural Genomics (JCSG)
History
DepositionAug 20, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 19, 2012Provider: 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 / struct_conn ...database_2 / 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

Downloads & links

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Assembly

Deposited unit
A: hypothetical protein
B: hypothetical protein
C: hypothetical protein
D: hypothetical protein
E: hypothetical protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)62,79616
Polymers61,7835
Non-polymers1,01311
Water10,251569
1
A: hypothetical protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)12,6334
Polymers12,3571
Non-polymers2763
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: hypothetical protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)12,6334
Polymers12,3571
Non-polymers2763
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: hypothetical protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)12,5413
Polymers12,3571
Non-polymers1842
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: hypothetical protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)12,5413
Polymers12,3571
Non-polymers1842
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
5
E: hypothetical protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)12,4492
Polymers12,3571
Non-polymers921
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)59.730, 59.730, 323.010
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number152
Space group name H-MP3121
Components on special symmetry positions
IDModelComponents
11B-314-

HOH

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Components

#1: Protein
hypothetical protein /


Mass: 12356.561 Da / Num. of mol.: 5
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Caulobacter crescentus (bacteria) / Strain: CB15 / Gene: 13422365, CC_1065 / Plasmid: SpeedET / Production host: Escherichia Coli (E. coli) / Strain (production host): PB1 / References: UniProt: Q9A9C4
#2: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 11 / Source method: obtained synthetically / Formula: C3H8O3
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 569 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsTHE CONSTRUCT WAS EXPRESSED WITH A PURIFICATION TAG MGSDKIHHHHHHENLYFQG. THE TAG WAS REMOVED WITH ...THE CONSTRUCT 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: 2.69 Å3/Da / Density % sol: 54.31 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7
Details: 0.2M magnesium chloride, 2.5M sodium chloride, 0.1M TRIS pH 7.0, NANODROP, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL11-1 / Wavelength: 0.97849,0.91837,0.97898
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jun 28, 2012
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
10.978491
20.918371
30.978981
ReflectionResolution: 1.87→49.262 Å / Num. obs: 56900 / % possible obs: 99.7 % / Observed criterion σ(I): -3 / Redundancy: 6.45 % / Biso Wilson estimate: 27.977 Å2 / Rmerge(I) obs: 0.075 / Net I/σ(I): 16.3
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. unique obs% possible all
1.87-1.946.520.9022.2737710578599.5
1.94-2.010.6163.332589501699.8
2.01-2.110.4324.638544611799.7
2.11-2.220.3136.4374495549100
2.22-2.360.2348.3371455638100
2.36-2.540.16311.134268552599.7
2.54-2.790.10915.937459556499.9
2.79-3.190.06723.536868569399.8
3.19-4.020.03837.837937586399.8
4.02-49.260.03245.836927615099.2

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Phasing

PhasingMethod: MAD

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Processing

Software
NameVersionClassificationNB
MolProbity3beta29model building
PDB_EXTRACT3.1data extraction
SHELXphasing
SHARPphasing
XSCALEMarch 15, 2012data scaling
BUSTER-TNT2.10.0refinement
XDSdata reduction
SHELXDphasing
BUSTER2.10.0refinement
RefinementMethod to determine structure: MAD / Resolution: 1.87→49.262 Å / Cor.coef. Fo:Fc: 0.9424 / Cor.coef. Fo:Fc free: 0.9324 / 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. ATOM RECORD CONTAINS SUM OF TLS AND RESIDUAL B FACTORS. ANISOU RECORD CONTAINS SUM OF TLS AND RESIDUAL U FACTORS. 3. THE MAD PHASES WERE USED AS RESTRAINTS DURING REFINEMENT. 4. GLYCEROL (GOL) MODELED ARE PRESENT IN CRYO CONDITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.2106 2872 5.06 %RANDOM
Rwork0.1803 ---
obs0.1818 56791 99.76 %-
Displacement parametersBiso max: 155.73 Å2 / Biso mean: 42.2962 Å2 / Biso min: 14.98 Å2
Baniso -1Baniso -2Baniso -3
1--4.3043 Å20 Å20 Å2
2---4.3043 Å20 Å2
3---8.6086 Å2
Refine analyzeLuzzati coordinate error obs: 0.265 Å
Refinement stepCycle: LAST / Resolution: 1.87→49.262 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4168 0 66 569 4803
Refine LS restraints
Refine-IDTypeNumberRestraint functionWeightDev ideal
X-RAY DIFFRACTIONt_dihedral_angle_d2110SINUSOIDAL2
X-RAY DIFFRACTIONt_trig_c_planes105HARMONIC2
X-RAY DIFFRACTIONt_gen_planes682HARMONIC5
X-RAY DIFFRACTIONt_it4420HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_chiral_improper_torsion575SEMIHARMONIC5
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_contact5352SEMIHARMONIC4
X-RAY DIFFRACTIONt_bond_d4420HARMONIC20.01
X-RAY DIFFRACTIONt_angle_deg5999HARMONIC20.89
X-RAY DIFFRACTIONt_omega_torsion3.24
X-RAY DIFFRACTIONt_other_torsion2.63
LS refinement shellResolution: 1.87→1.92 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.2591 210 5.15 %
Rwork0.2154 3871 -
all0.2176 4081 -
obs--99.76 %
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)
11.2922-0.24260.66220.5082-0.65452.0555-0.00730.0391-0.07480.00440.0417-0.0569-0.107-0.1147-0.0344-0.0727-0.0572-0.00910.0693-0.012-0.051243.2683-12.499241.7363
21.8118-0.1127-1.16660.7056-0.15882.10370.1151-0.05950.02440.0064-0.04950.015-0.0219-0.026-0.0656-0.07270.026-0.00590.07420.0059-0.06147.0962-7.419214.6379
31.14580.3434-0.94750.50130.30581.64590.06680.21280.026-0.03780.0144-0.01890.01950.0862-0.0811-0.0689-0.022-0.01410.1297-0.0057-0.065513.2759-7.692439.2948
44.02320.19742.75810.5558-0.09433.67030.21220.5187-0.2221-0.0368-0.04170.03860.12760.5592-0.1705-0.12280.0827-0.00940.1032-0.0491-0.145217.0123-12.178511.9056
53.1737-3.1169-0.98676.2912.18152.430.25850.1890.1155-0.4213-0.1594-0.2306-0.03480.2617-0.0991-0.05870.01170.0358-0.04070.0252-0.148334.066414.65741.7652
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1{A|2 - 109}A2 - 109
2X-RAY DIFFRACTION2{B|1 - 109}B1 - 109
3X-RAY DIFFRACTION3{C|1 - 108}C1 - 108
4X-RAY DIFFRACTION4{D|2 - 108}D2 - 108
5X-RAY DIFFRACTION5{E|2 - 108}E2 - 108

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