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- PDB-2g1u: CRYSTAL STRUCTURE OF A PUTATIVE TRANSPORT PROTEIN (TM1088A) FROM ... -

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Basic information

Entry
Database: PDB / ID: 2g1u
TitleCRYSTAL STRUCTURE OF A PUTATIVE TRANSPORT PROTEIN (TM1088A) FROM THERMOTOGA MARITIMA AT 1.50 A RESOLUTION
Componentshypothetical protein tm1088aHypothesis
KeywordsTRANSPORT PROTEIN / STRUCTURAL GENOMICS / JOINT CENTER FOR STRUCTURAL GENOMICS / JCSG / PROTEIN STRUCTURE INITIATIVE / PSI-2
Function / homologyNAD(P)-binding Rossmann-like Domain / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta / ADENOSINE MONOPHOSPHATE
Function and homology information
Biological speciesThermotoga maritima (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.5 Å
AuthorsJoint Center for Structural Genomics (JCSG)
CitationJournal: To be published
Title: Crystal structure of (tm1088a) from THERMOTOGA MARITIMA at 1.50 A resolution
Authors: Joint Center for Structural Genomics (JCSG)
History
DepositionFeb 14, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 28, 2006Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Advisory / Derived calculations / Version format compliance
Revision 1.3Aug 30, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_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_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Remark 999SEQUENCE: NO SUITABLE SEQUENCE DATABASE REFERENCE WAS AVAILABLE AT TIME OF PROCESSING THIS ENTRY.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: hypothetical protein tm1088a
hetero molecules


Theoretical massNumber of molelcules
Total (without water)18,1205
Polymers17,5131
Non-polymers6074
Water1,964109
1
A: hypothetical protein tm1088a
hetero molecules

A: hypothetical protein tm1088a
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,23910
Polymers35,0262
Non-polymers1,2138
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_656-x+1,y,-z+11
Buried area4920 Å2
ΔGint-95 kcal/mol
Surface area13540 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)47.859, 35.140, 56.579
Angle α, β, γ (deg.)90.000, 111.850, 90.000
Int Tables number3
Space group name H-MP121

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Components

#1: Protein hypothetical protein tm1088a / Hypothesis


Mass: 17512.998 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermotoga maritima (bacteria) / Gene: tm1088a / Production host: Escherichia coli (E. coli)
#2: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#3: Chemical ChemComp-AMP / ADENOSINE MONOPHOSPHATE / Adenosine monophosphate


Mass: 347.221 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H14N5O7P / Comment: AMP*YM
#4: Chemical ChemComp-MPD / (4S)-2-METHYL-2,4-PENTANEDIOL / 2-Methyl-2,4-pentanediol


Mass: 118.174 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H14O2 / Comment: precipitant*YM
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 109 / 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: 2.44 Å3/Da / Density % sol: 49.14 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop, nanodrop / pH: 6.5
Details: 40.0% MPD, 5.0% PEG-8000, 0.1M Cacodylate pH 6.5, VAPOR DIFFUSION,SITTING DROP,NANODROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.1 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Feb 4, 2005
RadiationMonochromator: Single crystal, cylindrically bent / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.5→44.421 Å / Num. obs: 26312 / % possible obs: 93.4 % / Redundancy: 5.1 % / Rmerge(I) obs: 0.048 / Rsym value: 0.048 / Net I/σ(I): 9.7
Reflection shell

Diffraction-ID: 1

Resolution (Å)% possible obs (%)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique obsRsym value% possible all
1.5-1.5463.81.50.3442.2195412980.34493.4
1.54-1.5874.91.70.3291.7251015120.329
1.58-1.6387.92.20.3392.2375916880.339
1.63-1.6896.22.80.2932.5511118430.293
1.68-1.7397.13.20.2413567617970.241
1.73-1.7997.63.60.1893.9622317290.189
1.79-1.8697.73.90.1315.5664417030.131
1.86-1.9497.94.10.1036.5649716030.103
1.94-2.0297.84.20.0797.5653715730.079
2.02-2.1298.54.20.0678.8626514960.067
2.12-2.2498.44.20.05910.4590814170.059
2.24-2.3799.37.20.097.21001313990.09
2.37-2.5499.87.70.0798.4985912870.079
2.54-2.7499.77.60.06410.3923012100.064
2.74-31007.60.0512.5848711220.05
3-3.3599.910.60.05610.81066910030.056
3.35-3.87100110.04414.2100229140.044
3.87-4.7499.910.70.0341882547680.034
4.74-6.7199.710.50.03417.363486020.034
6.71-44.4299.39.20.03615.331983480.036

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
REFMAC5.2.0005refinement
SCALAdata scaling
PDB_EXTRACT1.701data extraction
MOSFLMdata reduction
CCP4(SCALA)data scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1lss chain A

1lss


Resolution: 1.5→44.42 Å / Cor.coef. Fo:Fc: 0.974 / Cor.coef. Fo:Fc free: 0.966 / SU B: 2.396 / SU ML: 0.043 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.061 / ESU R Free: 0.062 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: (1) HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. (2) THE ASSIGNMENT OF NA ION WAS BASED ON COORDINATION, GEOMETRY, AND THE ABSENCE OF AN ANOMALOUS DIFFERENCE PEAK. (3) THERE ARE ...Details: (1) HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. (2) THE ASSIGNMENT OF NA ION WAS BASED ON COORDINATION, GEOMETRY, AND THE ABSENCE OF AN ANOMALOUS DIFFERENCE PEAK. (3) THERE ARE DIFFERENCE DENSITY PEAKS ALONG THE CRYSTALLOGRAPHIC 2-FOLD THAT WERE LEFT UNMODELED. (4) TLS GROUP PARTITIONING WAS AIDED BY TLSMD.
RfactorNum. reflection% reflectionSelection details
Rfree0.175 1332 5.1 %RANDOM
Rwork0.153 ---
all0.154 ---
obs0.15407 26310 93.03 %-
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: 15.075 Å2
Baniso -1Baniso -2Baniso -3
1--0.81 Å20 Å2-0.93 Å2
2--1.03 Å20 Å2
3----0.91 Å2
Refinement stepCycle: LAST / Resolution: 1.5→44.42 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1053 0 40 109 1202
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.0221216
X-RAY DIFFRACTIONr_bond_other_d0.0020.021124
X-RAY DIFFRACTIONr_angle_refined_deg1.6481.9841653
X-RAY DIFFRACTIONr_angle_other_deg0.82932623
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.1545158
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.57623.96253
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.09915227
X-RAY DIFFRACTIONr_dihedral_angle_4_deg11.71156
X-RAY DIFFRACTIONr_chiral_restr0.0980.2182
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.021342
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02263
X-RAY DIFFRACTIONr_nbd_refined0.2120.2207
X-RAY DIFFRACTIONr_nbd_other0.1840.21071
X-RAY DIFFRACTIONr_nbtor_refined0.1850.2591
X-RAY DIFFRACTIONr_nbtor_other0.0840.2708
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1430.280
X-RAY DIFFRACTIONr_metal_ion_refined0.0110.22
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.3330.210
X-RAY DIFFRACTIONr_symmetry_vdw_other0.1620.256
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.10.210
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined0.1050.22
X-RAY DIFFRACTIONr_mcbond_it1.6083715
X-RAY DIFFRACTIONr_mcbond_other0.4883296
X-RAY DIFFRACTIONr_mcangle_it2.77551168
X-RAY DIFFRACTIONr_scbond_it4.9368510
X-RAY DIFFRACTIONr_scangle_it7.60911475
LS refinement shellResolution: 1.5→1.539 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.375 61 -
Rwork0.261 1236 -
obs-1297 63.15 %
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)
13.6813-0.57821.28792.4591-0.33773.54220.1059-0.2571-0.14520.00920.01510.26470.1727-0.2989-0.1210.0612-0.0185-0.00530.0310.01590.08472.47831.70110.696
29.7573-7.09470.642210.376-0.65592.85580.16610.5073-0.3442-0.5108-0.06360.18480.3931-0.0174-0.10250.07820.0051-0.01490.0919-0.03720.042112.11231.678-1.68
32.62540.22820.33811.0810.08372.43160.0369-0.12110.01190.07510.0377-0.02050.02960.2446-0.07460.04310.01690.00940.08-0.01540.029118.87537.57510.539
42.7386-3.6874-3.09178.748211.828520.81180.0702-0.05590.1873-0.2760.0791-0.0312-0.61520.4024-0.14930.1117-0.05840.03360.0633-0.0097-0.008118.09343.56330.945
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION / Selection: ALL / Auth asym-ID: A / Label asym-ID: A

IDRefine TLS-IDAuth seq-IDLabel seq-ID
114 - 6016 - 72
2261 - 7273 - 84
3373 - 12385 - 135
44124 - 140136 - 152

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