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- PDB-4a35: Crystal structure of human Mitochondrial enolase superfamily memb... -

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Basic information

Entry
Database: PDB / ID: 4a35
TitleCrystal structure of human Mitochondrial enolase superfamily member 1 (ENOSF1)
ComponentsMITOCHONDRIAL ENOLASE SUPERFAMILY MEMBER 1
KeywordsISOMERASE
Function / homology
Function and homology information


: / L-fuconate dehydratase / L-fuconate dehydratase activity / amino acid catabolic process / hydro-lyase activity / carbohydrate catabolic process / isomerase activity / magnesium ion binding / mitochondrion
Similarity search - Function
L-fuconate dehydratase / Mandelate racemase / muconate lactonizing enzyme family signature 2. / Mandelate racemase/muconate lactonizing enzyme, conserved site / Mandelate racemase/muconate lactonizing enzyme, N-terminal domain / Mandelate racemase / muconate lactonizing enzyme, N-terminal domain / Mandelate racemase/muconate lactonizing enzyme, C-terminal / Mandelate racemase / muconate lactonizing enzyme, C-terminal domain / Enolase C-terminal domain-like / Enolase C-terminal domain-like / Enolase-like C-terminal domain ...L-fuconate dehydratase / Mandelate racemase / muconate lactonizing enzyme family signature 2. / Mandelate racemase/muconate lactonizing enzyme, conserved site / Mandelate racemase/muconate lactonizing enzyme, N-terminal domain / Mandelate racemase / muconate lactonizing enzyme, N-terminal domain / Mandelate racemase/muconate lactonizing enzyme, C-terminal / Mandelate racemase / muconate lactonizing enzyme, C-terminal domain / Enolase C-terminal domain-like / Enolase C-terminal domain-like / Enolase-like C-terminal domain / Enolase-like, N-terminal domain / Enolase-like, N-terminal / Enolase-like, C-terminal domain superfamily / Enolase-like; domain 1 / TIM Barrel / Alpha-Beta Barrel / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Mitochondrial enolase superfamily member 1
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.74 Å
AuthorsMuniz, J.R.C. / Froese, D.S. / Krojer, T. / Vollmar, M. / Canning, P. / von Delft, F. / Arrowsmith, C.H. / Edwards, A.M. / Weigelt, J. / Bountra, C. ...Muniz, J.R.C. / Froese, D.S. / Krojer, T. / Vollmar, M. / Canning, P. / von Delft, F. / Arrowsmith, C.H. / Edwards, A.M. / Weigelt, J. / Bountra, C. / Oppermann, U. / Yue, W.W.
CitationJournal: Biochemistry / Year: 2014
Title: Enzymatic and structural characterization of rTS gamma provides insights into the function of rTS beta.
Authors: Wichelecki, D.J. / Froese, D.S. / Kopec, J. / Muniz, J.R. / Yue, W.W. / Gerlt, J.A.
History
DepositionSep 30, 2011Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 12, 2011Provider: repository / Type: Initial release
Revision 1.1Dec 23, 2015Group: Database references
Revision 1.2Jan 16, 2019Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.journal_id_ISSN / _citation.page_last ..._citation.journal_id_ISSN / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.title / _citation_author.name
Revision 1.3May 8, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / 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_database_status.status_code_sf / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: MITOCHONDRIAL ENOLASE SUPERFAMILY MEMBER 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)50,05010
Polymers49,5671
Non-polymers4839
Water10,701594
1
A: MITOCHONDRIAL ENOLASE SUPERFAMILY MEMBER 1
hetero molecules

A: MITOCHONDRIAL ENOLASE SUPERFAMILY MEMBER 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)100,10020
Polymers99,1342
Non-polymers96618
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation12_554x,x-y,-z-1/61
Buried area7620 Å2
ΔGint-31.9 kcal/mol
Surface area29340 Å2
MethodPISA
Unit cell
Length a, b, c (Å)84.770, 84.770, 316.300
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number179
Space group name H-MP6522

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Components

#1: Protein MITOCHONDRIAL ENOLASE SUPERFAMILY MEMBER 1 / ENOLASE SUPERFAMILY MEMBER 1


Mass: 49567.141 Da / Num. of mol.: 1 / Fragment: RTSBETA, RESIDUES 1-440
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / Variant (production host): R3-PRARE2 / References: UniProt: Q7L5Y1, Isomerases
#2: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#3: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: C2H6O2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 594 / 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: 3.32 Å3/Da / Density % sol: 62.97 % / Description: NONE
Crystal growDetails: 25% PEG 3350, 0.1 M BIS-TRIS 5.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.97625, 0.9762
DetectorType: ADSC CCD / Detector: CCD / Date: Apr 25, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.976251
20.97621
ReflectionResolution: 1.74→19.99 Å / Num. obs: 69165 / % possible obs: 99 % / Observed criterion σ(I): 2.3 / Redundancy: 10.4 % / Biso Wilson estimate: 25.8 Å2 / Rmerge(I) obs: 0.04 / Net I/σ(I): 12.6
Reflection shellResolution: 1.74→1.84 Å / Redundancy: 8.3 % / Rmerge(I) obs: 0.79 / Mean I/σ(I) obs: 2.3 / % possible all: 93.9

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Processing

Software
NameVersionClassification
BUSTER2.10.0refinement
MOSFLMdata reduction
SCALEPACKdata scaling
SHARPphasing
RefinementMethod to determine structure: SAD
Starting model: NONE

Resolution: 1.74→19.99 Å / Cor.coef. Fo:Fc: 0.9668 / Cor.coef. Fo:Fc free: 0.9603 / SU R Cruickshank DPI: 0.075 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.082 / SU Rfree Blow DPI: 0.08 / SU Rfree Cruickshank DPI: 0.075
RfactorNum. reflection% reflectionSelection details
Rfree0.1756 3460 5.01 %RANDOM
Rwork0.1523 ---
obs0.1535 69027 98.45 %-
Displacement parametersBiso mean: 26.91 Å2
Baniso -1Baniso -2Baniso -3
1--0.6298 Å20 Å20 Å2
2---0.6298 Å20 Å2
3---1.2596 Å2
Refine analyzeLuzzati coordinate error obs: 0.171 Å
Refinement stepCycle: LAST / Resolution: 1.74→19.99 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3468 0 30 594 4092
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.0153640HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.114933HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d1716SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes91HARMONIC2
X-RAY DIFFRACTIONt_gen_planes530HARMONIC5
X-RAY DIFFRACTIONt_it3640HARMONIC20
X-RAY DIFFRACTIONt_nbd1SEMIHARMONIC5
X-RAY DIFFRACTIONt_omega_torsion4.51
X-RAY DIFFRACTIONt_other_torsion2.78
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion464SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact4938SEMIHARMONIC4
LS refinement shellResolution: 1.74→1.78 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.2879 217 5.44 %
Rwork0.24 3770 -
all0.2425 3987 -
obs--98.45 %
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)
1-0.3325-0.1779-1.33161.9224-1.5820.6390.0122-0.0876-0.06150.0768-0.0232-0.03670.07840.14240.0110.0753-0.028-0.0898-0.07750.01580.034466.81068.6352-15.2341
20.83370.1734-0.0041-0.07760.02080.79260.0515-0.0643-0.10580.04440.01010.06980.1355-0.107-0.0616-0.0381-0.0325-0.0051-0.03150.0435-0.021758.122328.264-14.7007
30.45570.13870.11380.17620.06750.40140.0296-0.0181-0.15180.0180.0264-0.03920.15280.0739-0.0561-0.01460.0054-0.0346-0.01660.0110.023975.780323.3622-19.6636
4-0.15740.12550.53280.5409-0.65340.00290.0373-0.00550.0042-0.07960.0185-0.0155-0.00920.1058-0.0558-0.03790.0576-0.04830.0701-0.00510.015693.027626.5968-11.2814
51.2944-0.7159-0.0661.5320.07640.35870.0873-0.217-0.10970.22630.01280.12730.02350.019-0.1001-0.0168-0.02930.01530.02510.0127-0.060471.9340.28764.312
60.68930.1589-0.17731.1047-0.24251.16590.0724-0.11680.17180.11880.00560.0069-0.21730.0926-0.078-0.0122-0.03760.0181-0.0228-0.0293-0.002472.915354.7837-8.015
70.2956-0.04530.22040.38070.02310.60980.0423-0.1214-0.05010.05650.0280.0170.06490.0264-0.0703-0.0469-0.0145-0.0197-0.00040.0261-0.017673.640833.2559-7.2682
84.245-1.1889-0.80794.33762.16100.0193-0.0466-0.13910.0322-0.127-0.03870.0039-0.25790.1077-0.0391-0.0320.01840.08390.0421-0.017143.64331.8422-9.688
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1CHAIN A AND (RESSEQ 4:12)
2X-RAY DIFFRACTION2CHAIN A AND (RESSEQ 13:84)
3X-RAY DIFFRACTION3CHAIN A AND (RESSEQ 85:169)
4X-RAY DIFFRACTION4CHAIN A AND (RESSEQ 170:174)
5X-RAY DIFFRACTION5CHAIN A AND (RESSEQ 175:224)
6X-RAY DIFFRACTION6CHAIN A AND (RESSEQ 225:310)
7X-RAY DIFFRACTION7CHAIN A AND (RESSEQ 311:427)
8X-RAY DIFFRACTION8CHAIN A AND (RESSEQ 428:444)

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