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- PDB-1p1m: Structure of Thermotoga maritima amidohydrolase TM0936 bound to N... -

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Basic information

Entry
Database: PDB / ID: 1p1m
TitleStructure of Thermotoga maritima amidohydrolase TM0936 bound to Ni and methionine
ComponentsHypothetical protein TM0936Hypothesis
KeywordsSTRUCTURAL GENOMICS / UNKNOWN FUNCTION / PUTATIVE METAL DEPENDENT HYDROLASE / PSI / Protein Structure Initiative / New York SGX Research Center for Structural Genomics / NYSGXRC
Function / homology
Function and homology information


S-adenosylhomocysteine deaminase / S-adenosylhomocysteine deaminase activity / S-methyl-5'-thioadenosine deaminase / 5'-methylthioadenosine deaminase activity / metal ion binding
Similarity search - Function
Deaminase MtaD/DadD / Urease, subunit C; domain 1 / Urease, subunit C, domain 1 / Amidohydrolase family / Metal-dependent hydrolase, composite domain superfamily / Amidohydrolase-related / Metal-dependent hydrolases / Metal-dependent hydrolase / Roll / TIM Barrel ...Deaminase MtaD/DadD / Urease, subunit C; domain 1 / Urease, subunit C, domain 1 / Amidohydrolase family / Metal-dependent hydrolase, composite domain superfamily / Amidohydrolase-related / Metal-dependent hydrolases / Metal-dependent hydrolase / Roll / TIM Barrel / Alpha-Beta Barrel / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
METHIONINE / NICKEL (II) ION / 5-methylthioadenosine/S-adenosylhomocysteine deaminase
Similarity search - Component
Biological speciesThermotoga maritima (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SIR / Resolution: 1.5 Å
AuthorsKniewel, R. / Buglino, J.A. / Lima, C.D. / Burley, S.K. / New York SGX Research Center for Structural Genomics (NYSGXRC)
CitationJournal: To be Published / Year: 2003
Title: Structure of the hypothetical protein TM0936 from Thermotoga maritima at 1.5A bound to Ni and methionine
Authors: Kniewel, R. / Buglino, J.A. / Lima, C.D.
History
DepositionApr 12, 2003Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 29, 2003Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 3, 2021Group: Derived calculations / Structure summary / Category: audit_author / struct_conn / struct_site
Item: _audit_author.identifier_ORCID / _struct_conn.ptnr1_auth_comp_id ..._audit_author.identifier_ORCID / _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
Revision 1.4Feb 14, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Hypothetical protein TM0936
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,0323
Polymers45,8241
Non-polymers2082
Water9,386521
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
A: Hypothetical protein TM0936
hetero molecules

A: Hypothetical protein TM0936
hetero molecules


Theoretical massNumber of molelcules
Total (without water)92,0656
Polymers91,6492
Non-polymers4164
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation5_675x-y+1,-y+2,-z+1/31
Buried area5830 Å2
ΔGint-47 kcal/mol
Surface area26620 Å2
MethodPISA
Unit cell
Length a, b, c (Å)113.373, 113.373, 79.884
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Cell settingtrigonal
Space group name H-MP3221

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Components

#1: Protein Hypothetical protein TM0936 / Hypothesis


Mass: 45824.355 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermotoga maritima (bacteria) / Gene: TM0936 / Plasmid: T7 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9X034
#2: Chemical ChemComp-NI / NICKEL (II) ION / Nickel


Mass: 58.693 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ni
#3: Chemical ChemComp-MET / METHIONINE / Methionine


Type: L-peptide linking / Mass: 149.211 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C5H11NO2S
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 521 / 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: 2

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Sample preparation

CrystalDensity Matthews: 2.83 Å3/Da / Density % sol: 56.2 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop
Details: 2.8M Sodium Formate, VAPOR DIFFUSION, HANGING DROP, temperature 291K

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
21101
Diffraction source
SourceSiteBeamlineTypeIDWavelength (Å)
SYNCHROTRONNSLS X4A10.979
ROTATING ANODERIGAKU RU20021.5418
Detector
TypeIDDetectorDate
ADSC QUANTUM 41CCDMar 28, 2003
RIGAKU RAXIS IV2IMAGE PLATEApr 1, 2003
Radiation
IDMonochromatorProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1Si(111)SINGLE WAVELENGTHMx-ray1
2OSMIC MULTILAYERSINGLE WAVELENGTHMx-ray1
Radiation wavelength
IDWavelength (Å)Relative weight
10.9791
21.54181
ReflectionResolution: 1.5→20 Å / Num. all: 94669 / Num. obs: 94669 / % possible obs: 99.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Biso Wilson estimate: 18.1 Å2 / Rmerge(I) obs: 0.082 / Net I/σ(I): 13
Reflection shellResolution: 1.5→1.55 Å / Redundancy: 4 % / Rmerge(I) obs: 0.358 / Mean I/σ(I) obs: 2.5 / Num. unique all: 9229 / % possible all: 97.9

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Processing

Software
NameVersionClassification
DENZOdata reduction
SCALEPACKdata scaling
SOLVEphasing
RESOLVEmodel building
CNS0.9refinement
RESOLVEphasing
RefinementMethod to determine structure: SIR / Resolution: 1.5→19.64 Å / Rfactor Rfree error: 0.003 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.213 4651 5 %RANDOM
Rwork0.201 ---
all0.2011 92422 --
obs0.2011 92422 97.5 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 63.3762 Å2 / ksol: 0.374708 e/Å3
Displacement parametersBiso mean: 23 Å2
Baniso -1Baniso -2Baniso -3
1--1.66 Å2-1.59 Å20 Å2
2---1.66 Å20 Å2
3---3.31 Å2
Refine analyzeLuzzati coordinate error free: 0.2 Å / Luzzati sigma a free: 0.17 Å
Refinement stepCycle: LAST / Resolution: 1.5→19.64 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3209 0 10 521 3740
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.005
X-RAY DIFFRACTIONc_angle_deg1.2
X-RAY DIFFRACTIONc_dihedral_angle_d23.1
X-RAY DIFFRACTIONc_improper_angle_d0.81
X-RAY DIFFRACTIONc_mcbond_it0.481.5
X-RAY DIFFRACTIONc_mcangle_it0.852
X-RAY DIFFRACTIONc_scbond_it0.772
X-RAY DIFFRACTIONc_scangle_it1.252.5
LS refinement shellResolution: 1.5→1.55 Å / Rfactor Rfree error: 0.014 / Total num. of bins used: 10
RfactorNum. reflection% reflection
Rfree0.288 440 5 %
Rwork0.29 8350 -
obs--93.6 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2DNA-RNA_REP.PARAMDNA-RNA.TOP
X-RAY DIFFRACTION3WATER_REP.PARAMWATER.TOP
X-RAY DIFFRACTION4ION.PARAMION.TOP

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