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- PDB-2f4p: Crystal structure of a cupin-like protein (tm1010) from thermotog... -

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Basic information

Entry
Database: PDB / ID: 2f4p
TitleCrystal structure of a cupin-like protein (tm1010) from thermotoga maritima msb8 at 1.90 A resolution
Componentshypothetical protein TM1010Hypothesis
KeywordsUNKNOWN FUNCTION / Double-stranded beta-helix fold / structural genomics / Joint Center for Structural Genomics / JCSG / Protein Structure Initiative / PSI-2
Function / homology
Function and homology information


Cupin 2, conserved barrel / Cupin domain / RmlC-like cupin domain superfamily / Jelly Rolls / RmlC-like jelly roll fold / Jelly Rolls / Sandwich / Mainly Beta
Similarity search - Domain/homology
Unknown ligand / : / Cupin_2 domain-containing protein
Similarity search - Component
Biological speciesThermotoga maritima (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.9 Å
AuthorsJoint Center for Structural Genomics (JCSG)
CitationJournal: To be published
Title: Crystal structure of hypothetical protein (tm1010) from THERMOTOGA MARITIMA at 1.90 A resolution
Authors: Joint Center for Structural Genomics (JCSG)
History
DepositionNov 23, 2005Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 24, 2006Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Advisory / Source and taxonomy / Version format compliance
Revision 1.3Jan 25, 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 TM1010
B: hypothetical protein TM1010
C: hypothetical protein TM1010
D: hypothetical protein TM1010
hetero molecules


Theoretical massNumber of molelcules
Total (without water)67,32218
Polymers66,7014
Non-polymers62114
Water9,044502
1
A: hypothetical protein TM1010
B: hypothetical protein TM1010
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,72310
Polymers33,3502
Non-polymers3728
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3730 Å2
ΔGint-7 kcal/mol
Surface area11810 Å2
MethodPISA
2
C: hypothetical protein TM1010
D: hypothetical protein TM1010
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,5998
Polymers33,3502
Non-polymers2486
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3230 Å2
ΔGint-12 kcal/mol
Surface area11800 Å2
MethodPISA
Unit cell
Length a, b, c (Å)71.746, 71.746, 188.600
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number170
Space group name H-MP65

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Components

#1: Protein
hypothetical protein TM1010 / Hypothesis


Mass: 16675.209 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermotoga maritima (bacteria) / Strain: MSB8 / Gene: tm1010 / Production host: Escherichia coli (E. coli) / References: GenBank: 4981537, UniProt: Q9X0A3*PLUS
#2: Chemical
ChemComp-UNL / UNKNOWN LIGAND


Num. of mol.: 4 / Source method: obtained synthetically
#3: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: C2H6O2
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 502 / 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: 2.07 Å3/Da / Density % sol: 40.23 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop, nanodrop / pH: 4
Details: 1.0M LiCl, 20.0% PEG-6000, 0.1M Citrate, pH 4.0, VAPOR DIFFUSION,SITTING DROP,NANODROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.2.1 / Wavelength: 1.000, 0.9797
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Sep 29, 2005 / Details: Collimating mirror, DCM, toroidal focusing mirror
RadiationMonochromator: Double Crystal Si(111) / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
111
20.97971
ReflectionResolution: 1.9→21.54 Å / Num. obs: 43148 / % possible obs: 99.9 % / Redundancy: 6.6 % / Biso Wilson estimate: 24.4 Å2 / Rmerge(I) obs: 0.083 / Rsym value: 0.083 / Net I/σ(I): 6.1
Reflection shell

Diffraction-ID: 1

Resolution (Å)% possible obs (%)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured obsRsym value% possible all
1.9-1.951006.10.5491.431820.54999.9
1.95-21006.60.4371.731020.437
2-2.061006.70.3132.430270.313
2.06-2.121006.70.2692.729350.269
2.12-2.191006.70.2083.528550.208
2.19-2.271006.70.1923.927410.192
2.27-2.361006.70.1714.326410.171
2.36-2.451006.70.1425.125550.142
2.45-2.561006.70.1275.724760.127
2.56-2.691006.70.1096.423230.109
2.69-2.831006.70.0887.722420.088
2.83-31006.70.0768.821160.076
3-3.211006.70.0679.419700.067
3.21-3.471006.60.05710.918520.057
3.47-3.81006.60.05510.917160.055
3.8-4.251006.60.05111.215370.051
4.25-4.911006.60.04910.513510.049
4.91-6.011006.50.05310.711590.053
6.01-8.51006.50.05610.38960.056
8.5-21.5493.660.05894720.058

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Phasing

PhasingMethod: MAD

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Processing

Software
NameVersionClassificationNB
REFMAC5.2.0005refinement
SCALAdata scaling
PDB_EXTRACT1.601data extraction
MOSFLMdata reduction
CCP4(SCALA)data scaling
SOLVEphasing
RefinementMethod to determine structure: MAD / Resolution: 1.9→21.54 Å / Cor.coef. Fo:Fc: 0.967 / Cor.coef. Fo:Fc free: 0.944 / SU B: 6.393 / SU ML: 0.1 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.146 / ESU R Free: 0.143
Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES
Details: 1. HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS 2. A MET-INHIBITION PROTOCOL WAS USED FOR SELENOMETHIONINE INCORPORATION DURING PROTEIN EXPRESSION. THE OCCUPANCY OF THE SE ATOMS IN THE ...Details: 1. HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS 2. 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 TO ACCOUNT FOR THE REDUCED SCATTERING POWER DUE TO PARTIAL S-MET INCORPORATION. 3. ELECTRON DENSITY AT THE PUTATIVE ACTIVE SITE WAS MODELED AS UNKNOWN LIGANDS. 4. DIFFERENCE ELECTRON DENSITY PEAKS WERE LOCATED WITHIN COVALENT BONDING DISTANCE OF THE SIDECHAINS OF GLN A58 AND GLN D58. THESE PEAKS WERE NOT MODELED.
RfactorNum. reflection% reflectionSelection details
Rfree0.216 2172 5 %RANDOM
Rwork0.16 ---
all0.163 ---
obs0.164 40900 100 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 34.607 Å2
Baniso -1Baniso -2Baniso -3
1-0.24 Å20.12 Å20 Å2
2--0.24 Å20 Å2
3----0.36 Å2
Refinement stepCycle: LAST / Resolution: 1.9→21.54 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4103 0 77 502 4682
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0214458
X-RAY DIFFRACTIONr_bond_other_d0.0030.023914
X-RAY DIFFRACTIONr_angle_refined_deg1.4671.9236086
X-RAY DIFFRACTIONr_angle_other_deg0.85739060
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.7595566
X-RAY DIFFRACTIONr_dihedral_angle_2_deg29.92223.515202
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.43515647
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.5031522
X-RAY DIFFRACTIONr_chiral_restr0.0940.2645
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.025044
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02946
X-RAY DIFFRACTIONr_nbd_refined0.1940.3824
X-RAY DIFFRACTIONr_nbd_other0.1730.33968
X-RAY DIFFRACTIONr_nbtor_refined0.1820.52171
X-RAY DIFFRACTIONr_nbtor_other0.0860.52488
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1890.5693
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1040.36
X-RAY DIFFRACTIONr_symmetry_vdw_other0.1970.370
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1390.535
X-RAY DIFFRACTIONr_mcbond_it2.04432858
X-RAY DIFFRACTIONr_mcbond_other0.54631136
X-RAY DIFFRACTIONr_mcangle_it2.74454370
X-RAY DIFFRACTIONr_scbond_it4.9581989
X-RAY DIFFRACTIONr_scangle_it6.762111700
LS refinement shellResolution: 1.9→1.949 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.263 168 -
Rwork0.177 2976 -
obs--100 %
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)
11.44470.39790.60492.31381.27672.3890.01140.0249-0.1298-0.01380.0662-0.1478-0.0359-0.0237-0.0776-0.2774-0.006-0.0171-0.254-0.0211-0.189837.12941.25627.457
222.457210.94912.18121.4115-5.76419.19690.53720.2935-1.41090.5755-0.277-0.49180.25520.4305-0.2602-0.15880.0418-0.0863-0.2251-0.0795-0.00940.24128.39326.612
34.2404-1.0532-0.30330.9727-0.35360.28030.088-0.10850.1540.0862-0.12620.1247-0.0489-0.24220.0382-0.12090.0817-0.0732-0.1917-0.0287-0.20131.10252.23828.24
42.46240.3482-0.40783.8435-0.45080.91760.06940.10940.01580.04480.07850.04470.0973-0.1037-0.1479-0.15560.0805-0.089-0.14080.0074-0.164319.44157.98120.749
53.1492-2.2531-0.30093.6075-0.52810.30570.02790.1049-0.0278-0.382-0.0890.0183-0.1539-0.13870.0611-0.23360.00110.0294-0.0773-0.0849-0.199344.46468.8161.552
63.2470.989-0.2843.0561-0.79490.6214-0.00620.0584-0.03710.03940.12860.0298-0.12390.0061-0.1224-0.21360.04420.049-0.0777-0.0745-0.164331.55477.82911.418
71.8170.51210.64192.10510.98592.26850.03680.0194-0.07830.030.0227-0.18060.0174-0.0864-0.0595-0.2533-0.0001-0.0104-0.273-0.0279-0.196154.11970.5974.775
89.29275.084-0.11818.98930.1992.82710.0809-0.18750.1490.15080.08650.01330.2747-0.1273-0.1675-0.2176-0.0002-0.0422-0.2416-0.0451-0.260454.70668.8938.976
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION / Selection: all

IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11AA2 - 12314 - 135
22AA124 - 135136 - 147
33BB4 - 4216 - 54
44BB43 - 13555 - 147
55CC3 - 4815 - 60
66CC49 - 13561 - 147
77DD3 - 11215 - 124
88DD113 - 135125 - 147

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