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- PDB-4noc: The crystal structure of a CBS Domain-containing Protein of Unkno... -

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Basic information

Entry
Database: PDB / ID: 4noc
TitleThe crystal structure of a CBS Domain-containing Protein of Unknown Function from Kribbella flavida DSM 17836.
ComponentsPutative signal transduction protein with CBS domains
KeywordsSIGNALING PROTEIN / structural genomics / PSI-Biology / protein structure initiative / midwest center for structural genomics / MCSG
Function / homology
Function and homology information


: / CBS-domain / CBS-domain / Domain in cystathionine beta-synthase and other proteins. / CBS domain superfamily / CBS domain / CBS domain / CBS domain profile. / Roll / Alpha Beta
Similarity search - Domain/homology
Putative signal transduction protein with CBS domains
Similarity search - Component
Biological speciesKribbella flavida (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.3 Å
AuthorsTan, K. / Hatzos-Skintges, C. / Jedrzejczak, R. / Joachimiak, A. / Midwest Center for Structural Genomics (MCSG)
CitationJournal: To be Published
Title: The crystal structure of a CBS Domain-containing Protein of Unknown Function from Kribbella flavida DSM 17836.
Authors: Tan, K. / Hatzos-Skintges, C. / Jedrzejczak, R. / Joachimiak, A.
History
DepositionNov 19, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 27, 2013Provider: repository / Type: Initial release
Revision 1.1Oct 30, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / 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_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _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: Putative signal transduction protein with CBS domains
B: Putative signal transduction protein with CBS domains
C: Putative signal transduction protein with CBS domains
D: Putative signal transduction protein with CBS domains
hetero molecules


Theoretical massNumber of molelcules
Total (without water)66,63516
Polymers65,4824
Non-polymers1,15312
Water2,324129
1
A: Putative signal transduction protein with CBS domains
B: Putative signal transduction protein with CBS domains
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,2217
Polymers32,7412
Non-polymers4805
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4730 Å2
ΔGint-98 kcal/mol
Surface area13450 Å2
MethodPISA
2
C: Putative signal transduction protein with CBS domains
hetero molecules

C: Putative signal transduction protein with CBS domains
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,70212
Polymers32,7412
Non-polymers96110
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation6_555x,-y+1/2,-z+1/41
Buried area5740 Å2
ΔGint-142 kcal/mol
Surface area13250 Å2
MethodPISA
3
D: Putative signal transduction protein with CBS domains
hetero molecules

D: Putative signal transduction protein with CBS domains
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,1256
Polymers32,7412
Non-polymers3844
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation10_555-x,-y,z1
Buried area4730 Å2
ΔGint-81 kcal/mol
Surface area13490 Å2
MethodPISA
Unit cell
Length a, b, c (Å)99.434, 99.434, 260.582
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number98
Space group name H-MI4122
Detailsexperimentally unknown. It is predicted that the chains A and B form a dimer. The chain C and its symmetry related molecule by the operator of ( x,-y+1/2,-z+1/4) form a dimer. The chain D and its symmetry related molecule by the operator of ( -x,-y,z) form a dimer.

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Components

#1: Protein
Putative signal transduction protein with CBS domains


Mass: 16370.454 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Kribbella flavida (bacteria) / Strain: DSM 17836 / Gene: Kfla_0464 / Plasmid: pMCSG73 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)magic / References: UniProt: D2PVT0
#2: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 129 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 2.46 Å3/Da / Density % sol: 49.98 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 4.5
Details: 1.6M Ammomnium Sulfate (diabasic), 0.1M Sodium acetate/Acetate acid and 0.2M Sodium Chloride., pH 4.5, VAPOR DIFFUSION, SITTING DROP, temperature 289K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-BM / Wavelength: 0.97929, 0.97945
DetectorType: ADSC QUANTUM 210r / Detector: CCD / Date: Nov 2, 2012 / Details: mirror
RadiationMonochromator: Si 111 crystal / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.979291
20.979451
ReflectionResolution: 2.3→40 Å / Num. all: 29395 / Num. obs: 29395 / % possible obs: 99.3 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -5 / Redundancy: 6 % / Biso Wilson estimate: 51.5 Å2 / Rmerge(I) obs: 0.072 / Net I/σ(I): 36.1
Reflection shellResolution: 2.3→2.34 Å / Redundancy: 6.2 % / Rmerge(I) obs: 0.619 / Mean I/σ(I) obs: 3.2 / Num. unique all: 1447 / % possible all: 100

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Processing

Software
NameVersionClassification
SBC-Collectdata collection
SHELXDphasing
MLPHAREphasing
DMmodel building
ARPmodel building
WARPmodel building
HKL-3000phasing
PHENIX(phenix.refine: 1.8.2_1309)refinement
HKL-3000data reduction
HKL-3000data scaling
DMphasing
RefinementMethod to determine structure: MAD / Resolution: 2.3→39.522 Å / SU ML: 0.29 / σ(F): 1.34 / Phase error: 25.04 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2398 1488 5.07 %random
Rwork0.1925 ---
all0.1949 29346 --
obs0.1949 29346 99.25 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.3→39.522 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4158 0 60 129 4347
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0084264
X-RAY DIFFRACTIONf_angle_d1.0985840
X-RAY DIFFRACTIONf_dihedral_angle_d12.0061521
X-RAY DIFFRACTIONf_chiral_restr0.066750
X-RAY DIFFRACTIONf_plane_restr0.005740
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.2992-2.37340.31621270.25762485X-RAY DIFFRACTION99
2.3734-2.45820.31621580.23332480X-RAY DIFFRACTION100
2.4582-2.55660.32061150.22832532X-RAY DIFFRACTION100
2.5566-2.6730.26211480.22372475X-RAY DIFFRACTION100
2.673-2.81390.29161210.22452537X-RAY DIFFRACTION100
2.8139-2.99010.28681350.22592523X-RAY DIFFRACTION100
2.9901-3.22090.27931520.21732532X-RAY DIFFRACTION100
3.2209-3.54480.25421480.19192533X-RAY DIFFRACTION100
3.5448-4.05730.21691310.16982559X-RAY DIFFRACTION100
4.0573-5.110.18681180.14912624X-RAY DIFFRACTION100
5.11-39.52820.21951350.20332578X-RAY DIFFRACTION94
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)
19.7781-2.1047-5.85367.57120.51763.7066-0.43670.228-1.0095-0.34040.0723-0.01710.7250.3520.32930.3746-0.028-0.09070.287-0.07360.4548-31.139-17.462544.134
22.60012.28871.05897.8852-1.02858.41350.5524-0.06230.18270.8001-0.47770.0164-0.0827-0.3273-0.20560.41350.06340.00460.3788-0.12420.3114-34.6774-8.745765.0579
38.19382.20921.70844.3639-1.07059.09160.05230.1886-0.09710.12430.06070.00570.22150.0821-0.17270.28450.08450.01310.4353-0.11920.3134-30.1374-5.134759.4034
47.29090.44623.7472.87591.65696.1296-0.1566-1.32710.65320.83290.3768-0.4953-0.40310.32050.02080.65110.0235-0.03770.6607-0.31270.519-24.55620.151574.5686
50.0639-0.4503-0.37362.88712.19381.8420.3696-0.77670.3431-0.4509-0.10430.11-1.54240.4129-0.08610.7481-0.0844-0.06690.3425-0.4733-0.302-28.66841.577553.7961
64.5171-2.247-2.97455.212-0.11824.3981-0.17670.0962-0.10680.26330.2247-0.0041-0.0079-0.1932-0.07090.20580.0347-0.08080.2716-0.09220.3061-26.7161-12.249841.9195
78.2458-0.2752-6.20893.0161-2.39568.2938-0.5224-0.5692-0.73910.463-0.0376-0.08760.17470.39150.47050.65830.1644-0.36120.9512-0.13580.7183-8.8542-16.750963.7462
85.3461-1.00092.95891.0116-0.78724.57950.0472-0.5373-0.15220.46390.3724-0.34710.41880.9341-0.34240.42280.1392-0.1660.6017-0.18840.5843-9.7793-14.258150.5847
97.6607-1.56231.73213.088-1.78279.1249-0.04370.17190.61360.0520.238-0.4269-0.39570.0626-0.14850.2284-0.03980.0450.2964-0.10120.3717-19.4919-7.007529.7457
105.18113.06853.02091.91430.84048.4739-0.48230.40630.1497-0.16840.4905-0.3205-0.52182.1008-0.08350.40040.0544-0.07010.5584-0.13440.6305-6.9831-11.278343.5747
113.76530.0173-5.06019.55682.45297.4445-0.6338-0.8412-0.06780.26640.8054-1.44170.68590.8471-0.2990.4435-0.028-0.13860.9999-0.23350.7092-11.5974-6.549172.3775
125.619-2.221.03786.98380.54974.52520.1826-0.9828-0.0334-0.16990.1869-0.60690.09270.0412-0.26110.41360.1611-0.16680.6787-0.14140.368-15.2654-11.879167.4012
132.712-1.618-0.09489.8014-6.10264.5962-0.3320.2579-0.5992-0.48261.32331.3741-0.2952-1.3023-0.79440.6109-0.1178-0.15990.4229-0.03030.4514-43.739913.958423.4196
145.59611.1316-1.00827.2391-0.23443.39920.3350.1341-0.0201-0.4583-0.11350.44380.3117-0.0843-0.14860.3818-0.0512-0.13040.36240.02150.2515-39.109127.28920.7197
152.93722.19544.07523.10334.09346.4524-0.2978-0.2638-0.27450.41120.4363-0.63620.6050.5361-0.2380.3196-0.07760.0720.43010.00050.356-28.085846.052427.638
163.29873.84332.94454.86633.41442.5401-0.520.54060.5202-1.33260.34621.0926-0.01780.27310.080.5957-0.1028-0.12350.48840.12040.4638-37.866146.310319.8549
174.49273.4257-3.21846.5561-1.20842.7297-0.42990.4227-0.5241-0.93630.6207-1.3879-0.20770.3324-0.02280.4987-0.20420.02460.4446-0.07350.43-32.14227.208516.6775
186.4495-1.55920.28265.8458-1.9368.7342-0.05520.1317-0.7021-0.4910.29490.66330.97620.1617-0.07630.31650.0877-0.02960.23510.01830.3287-34.85687.121530.8377
196.6144-1.23110.43526.5635-1.40218.9894-0.00220.2203-0.3981-0.12560.1470.5124-0.2126-0.431-0.18930.23770.0661-0.02180.19150.02510.305-41.170411.88530.1133
209.1565-6.04982.17396.0235-4.79165.91950.19131.158-0.6495-0.8155-0.17420.3670.1725-0.2761-0.10330.4668-0.17450.03780.6405-0.21480.5316-10.7222-8.892114.2874
214.0552.43871.44674.86640.35421.7568-0.37391.2552-0.2182-0.37470.1408-0.2943-0.01560.01690.28410.3214-0.09310.04930.5505-0.12760.53180.3098-12.04219.5141
226.1609-0.644-3.77358.0337-1.76495.597-0.382-0.1593-1.1656-0.0687-0.26380.1390.12820.44650.54650.4019-0.0075-0.15430.51160.03170.715222.3243-8.429226.7187
233.1047-2.6561-0.45617.06510.90196.2527-0.4849-0.7-1.20580.03750.2024-0.1730.64450.51040.33490.4839-0.05490.00150.3607-0.03930.66433.4137-15.707624.5685
249.1816-1.66950.66293.1922-1.16286.19660.06290.87390.41090.04590.04940.5631-0.3584-0.2074-0.0310.2961-0.10430.05950.4243-0.01630.4313-18.49760.194921.7326
256.9822.00260.07138.6917-0.80114.546-0.44440.59020.6732-0.88690.22120.38080.32980.0970.20670.2596-0.12010.030.6726-0.08010.4955-13.1285-2.53516.3505
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 1 through 11 )
2X-RAY DIFFRACTION2chain 'A' and (resid 12 through 28 )
3X-RAY DIFFRACTION3chain 'A' and (resid 29 through 56 )
4X-RAY DIFFRACTION4chain 'A' and (resid 57 through 91 )
5X-RAY DIFFRACTION5chain 'A' and (resid 92 through 100 )
6X-RAY DIFFRACTION6chain 'A' and (resid 101 through 148 )
7X-RAY DIFFRACTION7chain 'B' and (resid 1 through 18 )
8X-RAY DIFFRACTION8chain 'B' and (resid 19 through 56 )
9X-RAY DIFFRACTION9chain 'B' and (resid 57 through 74A)
10X-RAY DIFFRACTION10chain 'B' and (resid 75 through 100 )
11X-RAY DIFFRACTION11chain 'B' and (resid 101 through 117 )
12X-RAY DIFFRACTION12chain 'B' and (resid 118 through 145 )
13X-RAY DIFFRACTION13chain 'C' and (resid 0 through 18 )
14X-RAY DIFFRACTION14chain 'C' and (resid 19 through 56 )
15X-RAY DIFFRACTION15chain 'C' and (resid 57 through 69 )
16X-RAY DIFFRACTION16chain 'C' and (resid 70 through 83 )
17X-RAY DIFFRACTION17chain 'C' and (resid 84 through 99 )
18X-RAY DIFFRACTION18chain 'C' and (resid 100 through 118 )
19X-RAY DIFFRACTION19chain 'C' and (resid 119 through 146 )
20X-RAY DIFFRACTION20chain 'D' and (resid 1 through 18 )
21X-RAY DIFFRACTION21chain 'D' and (resid 19 through 56 )
22X-RAY DIFFRACTION22chain 'D' and (resid 57 through 76 )
23X-RAY DIFFRACTION23chain 'D' and (resid 77 through 100 )
24X-RAY DIFFRACTION24chain 'D' and (resid 101 through 118 )
25X-RAY DIFFRACTION25chain 'D' and (resid 119 through 145 )

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