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- PDB-1o5u: Crystal structure of a duf861 family protein (tm1112) from thermo... -

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Basic information

Entry
Database: PDB / ID: 1o5u
TitleCrystal structure of a duf861 family protein (tm1112) from thermotoga maritima at 1.83 A resolution
Componentsnovel Thermotoga maritima enzyme TM1112
KeywordsUNKNOWN FUNCTION / Cupin / novel thermotoga maritima enzyme / structural genomics / Joint Center for Structural Genomics / JCSG / Protein Structure Initiative / PSI
Function / homology
Function and homology information


(S)-ureidoglycine aminohydrolase, cupin domain / EutQ-like 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 / (S)-ureidoglycine aminohydrolase cupin domain-containing protein
Similarity search - Component
Biological speciesThermotoga maritima (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.83 Å
AuthorsJoint Center for Structural Genomics (JCSG)
CitationJournal: Proteins / Year: 2004
Title: Crystal structure of a novel Thermotoga maritima enzyme (TM1112) from the cupin family at 1.83 A resolution
Authors: McMullan, D. / Schwarzenbacher, R. / Jaroszewski, L. / von Delft, F. / Klock, H.E. / Vincent, J. / Quijano, K. / Abdubek, P. / Ambing, E. / Biorac, T. / Brinen, L.S. / Canaves, J.M. / Dai, X. ...Authors: McMullan, D. / Schwarzenbacher, R. / Jaroszewski, L. / von Delft, F. / Klock, H.E. / Vincent, J. / Quijano, K. / Abdubek, P. / Ambing, E. / Biorac, T. / Brinen, L.S. / Canaves, J.M. / Dai, X. / Deacon, A.M. / DiDonato, M. / Elsliger, M.A. / Eshaghi, S. / Floyd, R. / Godzik, A. / Grittini, C. / Grzechnik, S.K. / Hampton, E. / Karlak, C. / Koesema, E. / Kreusch, A. / Kuhn, P. / Levin, I. / McPhillips, T.M. / Miller, M.D. / Morse, A. / Moy, K. / Ouyang, J. / Page, R. / Reyes, R. / Rezezadeh, F. / Robb, A. / Sims, E. / Spraggon, G. / Stevens, R.C. / van den Bedem, H. / Velasquez, J. / Wang, X. / West, B. / Wolf, G. / Xu, Q. / Hodgson, K.O. / Wooley, J. / Lesley, S.A. / Wilson, I.A.
History
DepositionOct 6, 2003Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 11, 2003Provider: repository / Type: Initial release
Revision 1.1Apr 26, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.3Jul 18, 2018Group: Data collection / Database references / Category: pdbx_database_related
Revision 1.4Jan 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
Revision 1.5Sep 20, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Remark 600HETEROGEN THE UNIDENTIFIABLE SPECIES COVALENTLY BOUND TO LYS84 HAS BEEN MODELED AS RESIDUE UNL, ...HETEROGEN THE UNIDENTIFIABLE SPECIES COVALENTLY BOUND TO LYS84 HAS BEEN MODELED AS RESIDUE UNL, UNKNOWN LIGAND, AND ATOM TYPE C TO ACCOUNT FOR THE SCATTERING STRENGTH.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: novel Thermotoga maritima enzyme TM1112
B: novel Thermotoga maritima enzyme TM1112


Theoretical massNumber of molelcules
Total (without water)24,4725
Polymers24,4722
Non-polymers03
Water5,080282
1
A: novel Thermotoga maritima enzyme TM1112


Theoretical massNumber of molelcules
Total (without water)12,2362
Polymers12,2361
Non-polymers01
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: novel Thermotoga maritima enzyme TM1112


Theoretical massNumber of molelcules
Total (without water)12,2363
Polymers12,2361
Non-polymers02
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)39.627, 74.729, 42.210
Angle α, β, γ (deg.)90.00, 91.02, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein novel Thermotoga maritima enzyme TM1112


Mass: 12236.052 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermotoga maritima (bacteria) / Gene: TM1112 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9X0J6
#2: Chemical ChemComp-UNL / UNKNOWN LIGAND


Num. of mol.: 3 / Source method: obtained synthetically
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 282 / 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: 2.48 Å3/Da / Density % sol: 49.95 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop, nanodrop
Details: 25.5% PEG-4000, 0.17M ammonium sulfate, 15% glycerol anhydrous , VAPOR DIFFUSION,SITTING DROP,NANODROP, temperature 277K
Crystal grow
*PLUS
pH: 7.9 / Method: vapor diffusion
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetailsChemical formula
120 mMTris1droppH7.9
2150 mM1dropNaCl
30.25 mMTCEP1drop
419 mg/mlprotein1drop
525.5 %PEG40001reservoir
615 %glycerol1reservoir
70.17 Mammonium sulfate1reservoir

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL9-1 / Wavelength: 0.97001
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Jun 3, 2001
RadiationMonochromator: single crystal Si(311) bent monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97001 Å / Relative weight: 1
ReflectionResolution: 1.81→36.76 Å / Num. all: 21322 / Num. obs: 21322 / % possible obs: 94.9 % / Redundancy: 2.6 % / Biso Wilson estimate: 36.92 Å2 / Rsym value: 0.045 / Net I/σ(I): 18
Reflection shellResolution: 1.81→1.85 Å / Redundancy: 1.8 % / Mean I/σ(I) obs: 3.1 / Num. unique all: 461 / Rsym value: 0.307 / % possible all: 34.6
Reflection
*PLUS
Highest resolution: 1.83 Å / Lowest resolution: 27.98 Å / % possible obs: 98.2 % / Num. measured all: 53783 / Rmerge(I) obs: 0.045
Reflection shell
*PLUS
Highest resolution: 1.83 Å / Lowest resolution: 1.86 Å / % possible obs: 84.6 % / Rmerge(I) obs: 0.307

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Processing

Software
NameVersionClassification
MOSFLMdata reduction
SCALA5.0)data scaling
MOLREPphasing
REFMAC5.1.9999refinement
CCP4(SCALA)data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1lkn

1lkn


Resolution: 1.83→27.98 Å / Cor.coef. Fo:Fc: 0.967 / Cor.coef. Fo:Fc free: 0.946 / SU B: 5.52 / SU ML: 0.087 / TLS residual ADP flag: LIKELY RESIDUAL / Isotropic thermal model: ISOTROPIC / Cross valid method: THROUGHOUT / ESU R: 0.119 / ESU R Free: 0.124 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: 1. HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. 2. THE UNIDENTIFIABLE SPECIES COVALENTLY BOUND TO LYS84 HAS BEEN MODELED AS RESIDUE UNL, UNKNOWN LIGAND, AND ATOM TYPE C TO ACCOUNT FOR ...Details: 1. HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. 2. THE UNIDENTIFIABLE SPECIES COVALENTLY BOUND TO LYS84 HAS BEEN MODELED AS RESIDUE UNL, UNKNOWN LIGAND, AND ATOM TYPE C TO ACCOUNT FOR THE SCATTERING STRENGTH.
RfactorNum. reflection% reflectionSelection details
Rfree0.22239 1071 5 %RANDOM
Rwork0.17011 ---
obs0.17277 20232 98.15 %-
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: 33.54 Å2
Baniso -1Baniso -2Baniso -3
1-0.84 Å20 Å20.38 Å2
2---0.86 Å20 Å2
3---0.04 Å2
Refinement stepCycle: LAST / Resolution: 1.83→27.98 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1504 0 13 282 1799
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0170.0221549
X-RAY DIFFRACTIONr_bond_other_d0.0010.021393
X-RAY DIFFRACTIONr_angle_refined_deg1.6491.9572097
X-RAY DIFFRACTIONr_angle_other_deg0.84233280
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.8845174
X-RAY DIFFRACTIONr_dihedral_angle_2_deg28.75124.72272
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.7115299
X-RAY DIFFRACTIONr_dihedral_angle_4_deg24.74156
X-RAY DIFFRACTIONr_chiral_restr0.1170.2222
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.021640
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02302
X-RAY DIFFRACTIONr_nbd_refined0.1940.2241
X-RAY DIFFRACTIONr_nbd_other0.1790.21367
X-RAY DIFFRACTIONr_nbtor_other0.0840.2941
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.0780.21
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2270.26
X-RAY DIFFRACTIONr_symmetry_vdw_other0.3430.228
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1910.218
X-RAY DIFFRACTIONr_mcbond_it1.361.51181
X-RAY DIFFRACTIONr_mcangle_it1.49621454
X-RAY DIFFRACTIONr_scbond_it2.8213930
X-RAY DIFFRACTIONr_scangle_it3.5064.5643
LS refinement shellResolution: 1.83→1.879 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.246 61 4.05 %
Rwork0.197 1445 -
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)
14.4003-0.36710.42842.2828-0.04492.02220.0301-0.28250.13170.17080.02870.15160.1839-0.0118-0.0588-0.1647-0.01960.0346-0.2042-0.0108-0.212913.2477-0.650312.6328
22.8504-0.004-0.93052.75970.46974.2698-0.06720.0387-0.24890.17870.0858-0.1594-0.06320.0994-0.0186-0.20880.0012-0.0437-0.19470.0203-0.181731.4617-19.48776.4856
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION / Selection: ALL / Auth seq-ID: 2 - 89 / Label seq-ID: 14 - 101

IDRefine TLS-IDAuth asym-IDLabel asym-ID
11AA
22BB
Refinement
*PLUS
Rfactor Rfree: 0.222 / Rfactor Rwork: 0.17
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONr_bond_d0.017
X-RAY DIFFRACTIONr_angle_d
X-RAY DIFFRACTIONr_angle_deg1.65

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