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- PDB-3no5: Crystal structure of a Pfam DUF849 domain containing protein (Reu... -

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Basic information

Entry
Database: PDB / ID: 3no5
TitleCrystal structure of a Pfam DUF849 domain containing protein (Reut_A1631) from Ralstonia eutropha JMP134 at 1.90 A resolution
ComponentsUncharacterized protein
KeywordsSTRUCTURAL GENOMICS / UNKNOWN FUNCTION / Pfam DUF849 domain containing protein / Joint Center for Structural Genomics / JCSG / Protein Structure Initiative / PSI-2
Function / homology
Function and homology information


3-keto-5-aminohexanoate cleavage activity / metal ion binding
Similarity search - Function
3-keto-5-aminohexanoate cleavage enzyme / beta-keto acid cleavage enzyme / Aldolase class I / Aldolase-type TIM barrel / TIM Barrel / Alpha-Beta Barrel / Alpha Beta
Similarity search - Domain/homology
ACETATE ION / 3-keto-5-aminohexanoate cleavage enzyme
Similarity search - Component
Biological speciesRalstonia eutropha (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / molecular replacement / Resolution: 1.9 Å
AuthorsJoint Center for Structural Genomics (JCSG)
CitationJournal: To be published
Title: Crystal structure of a Pfam DUF849 domain containing protein (Reut_A1631) from Ralstonia eutropha JMP134 at 1.90 A resolution
Authors: Joint Center for Structural Genomics (JCSG)
History
DepositionJun 24, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 25, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Source and taxonomy / Version format compliance
Revision 1.2Nov 8, 2017Group: Refinement description / Category: software
Revision 1.3Feb 1, 2023Group: Database references / Derived calculations
Category: database_2 / pdbx_struct_conn_angle ...database_2 / pdbx_struct_conn_angle / 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 / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _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_asym_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_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.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_asym_id / _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_asym_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_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Sep 20, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.5Nov 22, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond / Item: _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_2
Revision 1.6Nov 27, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Uncharacterized protein
B: Uncharacterized protein
C: Uncharacterized protein
D: Uncharacterized protein
E: Uncharacterized protein
F: Uncharacterized protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)182,01025
Polymers180,8206
Non-polymers1,19019
Water19,7441096
1
A: Uncharacterized protein
B: Uncharacterized protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)60,5286
Polymers60,2732
Non-polymers2554
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2910 Å2
ΔGint-71 kcal/mol
Surface area20470 Å2
MethodPISA
2
C: Uncharacterized protein
D: Uncharacterized protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)61,01614
Polymers60,2732
Non-polymers74212
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4470 Å2
ΔGint-74 kcal/mol
Surface area20250 Å2
MethodPISA
3
E: Uncharacterized protein
F: Uncharacterized protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)60,4665
Polymers60,2732
Non-polymers1933
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2690 Å2
ΔGint-73 kcal/mol
Surface area20860 Å2
MethodPISA
Unit cell
Length a, b, c (Å)83.181, 81.221, 140.429
Angle α, β, γ (deg.)90.000, 103.680, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
Uncharacterized protein


Mass: 30136.668 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Ralstonia eutropha (bacteria) / Strain: JMP134 / Gene: Reut_A1631 / Plasmid: SpeedET / Production host: Escherichia coli (E. coli) / Strain (production host): HK100 / References: UniProt: Q471D6
#2: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Zn
#3: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: C2H6O2
#4: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C2H3O2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1096 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY
Sequence detailsTHE CONSTRUCT (1-274) WAS EXPRESSED WITH A PURIFICATION TAG MGSDKIHHHHHHENLYFQG. THE TAG WAS ...THE CONSTRUCT (1-274) WAS EXPRESSED WITH A PURIFICATION TAG MGSDKIHHHHHHENLYFQG. THE TAG WAS REMOVED WITH TEV PROTEASE LEAVING ONLY A GLYCINE FOLLOWED BY THE TARGET SEQUENCE.

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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: 2.55 Å3/Da / Density % sol: 51.75 %
Crystal growTemperature: 277 K / pH: 6.33
Details: 18.0% polyethylene glycol 8000, 0.15M magnesium acetate, 0.1M sodium cacodylate pH 6.33, NANODROP, VAPOR DIFFUSION, SITTING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL11-1 / Wavelength: 0.91162
DetectorType: MARMOSAIC 325 mm CCD / Detector: CCD / Date: Feb 12, 2007 / Details: FLAT MIRROR (VERTICAL FOCUSING)
RadiationMonochromator: SINGLE CRYSTAL SI(111) BENT MONOCHROMATOR (HORIZONTAL FOCUSING)
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.91162 Å / Relative weight: 1
ReflectionResolution: 1.9→29.961 Å / Num. obs: 143033 / % possible obs: 99.9 % / Redundancy: 3.2 % / Rmerge(I) obs: 0.124 / Rsym value: 0.124 / Net I/σ(I): 9.2
Reflection shellResolution: 1.9→1.95 Å / Redundancy: 3.3 % / Rmerge(I) obs: 0.436 / Mean I/σ(I) obs: 1.7 / Rsym value: 0.436 / % possible all: 100

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
MolProbity3beta29model building
PHENIXrefinement
PHASERphasing
SCALA3.2.5data scaling
PDB_EXTRACT3.006data extraction
MOSFLMdata reduction
BUSTER2.8.0refinement
RefinementMethod to determine structure: molecular replacement
Starting model: 3CHV

3chv


Resolution: 1.9→29.96 Å / Cor.coef. Fo:Fc: 0.912 / Cor.coef. Fo:Fc free: 0.893 / Occupancy max: 1 / Occupancy min: 0.08 / Cross valid method: THROUGHOUT / σ(F): 0
Details: (1). A MET-INHIBITION PROTOCOL WAS USED FOR SELENOMETHIONINE INCORPORATION DURING PROTEIN EXPRESSION.0.75 TO ACCOUNT FOR THE REDUCED SCATTERING POWER DUE TO PARTIAL S-MET INCORPORATION. (2). ...Details: (1). A MET-INHIBITION PROTOCOL WAS USED FOR SELENOMETHIONINE INCORPORATION DURING PROTEIN EXPRESSION.0.75 TO ACCOUNT FOR THE REDUCED SCATTERING POWER DUE TO PARTIAL S-MET INCORPORATION. (2). THE MODELING OF ZINC IS SUPPORTED BY ANOMALOUS DIFFERENCE MAPS AND STRUCTURAL SIMILARITY TO A HOMOLOG, PDB ID 3CHV. (3).ACETATE (ACT) FROM THE CRYSTALLIZATION AND ETHYLENE GLYCOL(EDO) USED AS A CRYOPROTECTANT WERE MODELED INTO THE STRUCTURE.(4). ATOM RECORD CONTAINS SUM OF TLS AND RESIDUAL B FACTORS. (5). ANISOU RECORD CONTAINS SUM OF TLS AND RESIDUAL U FACTORS. (6). WATERS WERE EXCLUDED FROM TLS ASSIGNMENT.
RfactorNum. reflection% reflectionSelection details
Rfree0.224 7173 5.02 %RANDOM
Rwork0.206 ---
obs0.207 143012 --
Displacement parametersBiso mean: 26.69 Å2
Baniso -1Baniso -2Baniso -3
1--1.911 Å20 Å2-1.197 Å2
2--3.391 Å20 Å2
3----1.48 Å2
Refinement stepCycle: LAST / Resolution: 1.9→29.96 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms12246 0 58 1096 13400
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.00912901HARMONIC2
X-RAY DIFFRACTIONt_angle_deg0.5317617HARMONIC6
X-RAY DIFFRACTIONt_dihedral_angle_d4536SINUSOIDAL5
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes314HARMONIC2
X-RAY DIFFRACTIONt_gen_planes1979HARMONIC5
X-RAY DIFFRACTIONt_it12901HARMONIC20
X-RAY DIFFRACTIONt_nbd0SEMIHARMONIC5
X-RAY DIFFRACTIONt_omega_torsion3.47
X-RAY DIFFRACTIONt_other_torsion14.62
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion17595
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_contact16396SEMIHARMONIC4
LS refinement shellResolution: 1.9→1.95 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.231 529 5.03 %
Rwork0.204 9982 -
all0.206 10511 -
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)
11.06510.27150.09931.8653-0.16610.58110.0103-0.0421-0.15480.1877-0.0137-0.3826-0.0008-0.00910.00340.11180.0005-0.1458-0.18850.006-0.084834.22571.516264.6031
21.28-0.4294-0.16091.3813-0.20961.0479-0.203-0.1065-0.03490.43270.12560.1526-0.1257-0.12510.07740.23920.06350.0014-0.19180.0066-0.2054-0.34512.602876.8755
30.6546-0.4490.23751.2605-0.27071.4754-0.10320.04520.07840.16230.008-0.0573-0.36690.01990.09520.0718-0.0256-0.082-0.11530.0125-0.11068.839817.076135.5754
40.83990.2816-0.34541.30030.05611.0634-0.151-0.0534-0.15340.0023-0.0263-0.05540.26370.04120.17730.01280.00590.0332-0.09690.0299-0.063912.4604-16.90222.1431
50.9624-0.18790.39730.6895-0.04631.1228-0.1027-0.1304-0.02920.15320.076-0.0133-0.0446-0.04430.02670.03160.02960.0069-0.0926-0.0021-0.066-23.426638.075419.3102
60.90880.48040.19371.67260.05910.6636-0.06350.02360.1669-0.05230.02880.3875-0.08-0.07280.0347-0.05060.00740.0002-0.12290.00590.0282-48.275739.5496-7.9319
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth seq-ID
1X-RAY DIFFRACTION10
2X-RAY DIFFRACTION20
3X-RAY DIFFRACTION30
4X-RAY DIFFRACTION40
5X-RAY DIFFRACTION50
6X-RAY DIFFRACTION60

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