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- PDB-4kpl: Crystal structure of d-mannonate dehydratase from chromohalobacte... -

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Basic information

Entry
Database: PDB / ID: 4kpl
TitleCrystal structure of d-mannonate dehydratase from chromohalobacter salexigens complexed with Mg,d-mannonate and 2-keto-3-deoxy-d-gluconate
ComponentsD-mannonate dehydratase
KeywordsHYDROLASE / Enolase fold / D-MANNONATE DEHYDRATASE / D-MANNONATE / 2-KETO-3-DEOXY-D-GLUCONATE
Function / homology
Function and homology information


gluconate dehydratase / gluconate dehydratase activity / mannonate dehydratase / mannonate dehydratase activity / Lyases; Carbon-oxygen lyases; Hydro-lyases / amino acid catabolic process / carbohydrate catabolic process / magnesium ion binding
Similarity search - Function
D-mannonate dehydratase-like / Mandelate racemase / muconate lactonizing enzyme family signature 1. / Mandelate racemase/muconate lactonizing enzyme, conserved site / Mandelate racemase DgoD-like / 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 ...D-mannonate dehydratase-like / Mandelate racemase / muconate lactonizing enzyme family signature 1. / Mandelate racemase/muconate lactonizing enzyme, conserved site / Mandelate racemase DgoD-like / 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
D-MANNONIC ACID / 2-KETO-3-DEOXYGLUCONATE / D-galactonate dehydratase family member ManD
Similarity search - Component
Biological speciesChromohalobacter salexigens (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsFedorov, A.A. / Fedorov, E.V. / Wichelecki, D. / Gerlt, J.A. / Almo, S.C.
CitationJournal: To be Published
Title: Crystal structure of d-mannonate dehydratase from chromohalobacter salexigens complexed with Mg,d-mannonate and 2-keto-3-deoxy-d-gluconate
Authors: Fedorov, A.A. / Fedorov, E.V. / Wichelecki, D. / Gerlt, J.A. / Almo, S.C.
History
DepositionMay 13, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 14, 2014Provider: repository / Type: Initial release
Revision 1.1Sep 20, 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_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_auth_seq_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.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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: D-mannonate dehydratase
B: D-mannonate dehydratase
C: D-mannonate dehydratase
D: D-mannonate dehydratase
E: D-mannonate dehydratase
F: D-mannonate dehydratase
G: D-mannonate dehydratase
H: D-mannonate dehydratase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)365,67229
Polymers363,7468
Non-polymers1,92621
Water34,6071921
1
A: D-mannonate dehydratase
E: D-mannonate dehydratase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)91,4137
Polymers90,9372
Non-polymers4765
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6360 Å2
ΔGint-35 kcal/mol
Surface area26450 Å2
MethodPISA
2
B: D-mannonate dehydratase
D: D-mannonate dehydratase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)91,3957
Polymers90,9372
Non-polymers4585
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6350 Å2
ΔGint-36 kcal/mol
Surface area26630 Å2
MethodPISA
3
C: D-mannonate dehydratase
G: D-mannonate dehydratase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)91,4698
Polymers90,9372
Non-polymers5326
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6680 Å2
ΔGint-36 kcal/mol
Surface area26260 Å2
MethodPISA
4
F: D-mannonate dehydratase
H: D-mannonate dehydratase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)91,3957
Polymers90,9372
Non-polymers4585
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6310 Å2
ΔGint-36 kcal/mol
Surface area26600 Å2
MethodPISA
Unit cell
Length a, b, c (Å)110.242, 167.263, 168.863
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

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Protein , 1 types, 8 molecules ABCDEFGH

#1: Protein
D-mannonate dehydratase


Mass: 45468.258 Da / Num. of mol.: 8
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Chromohalobacter salexigens (bacteria) / Strain: DSM 3043 / ATCC BAA-138 / NCIMB 13768 / Gene: Csal_2974 / Production host: Escherichia coli (E. coli) / References: UniProt: Q1QT89, mannonate dehydratase

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Non-polymers , 6 types, 1942 molecules

#2: Chemical
ChemComp-CS2 / D-MANNONIC ACID / D-MANNONATE


Mass: 196.155 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C6H12O7
#3: Chemical
ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Cl
#4: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: Mg
#5: Chemical
ChemComp-KDG / 2-KETO-3-DEOXYGLUCONATE


Mass: 178.140 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C6H10O6
#6: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#7: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 1921 / 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: 2.14 Å3/Da / Density % sol: 42.52 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 5.5
Details: 0.3 M MAGNESIUM FORMATE, 0.1M BIS-TRIS, pH 5.5, VAPOR DIFFUSION, SITTING DROP, temperature 293.0K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X29A / Wavelength: 0.979 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Oct 7, 2010
RadiationMonochromator: Si 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 2→41.816 Å / Num. all: 210043 / Num. obs: 210043 / % possible obs: 99.97 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0

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Processing

Software
NameVersionClassification
CBASSdata collection
BALBESphasing
PHENIX(phenix.refine: 1.7.1_743)refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3OW1

3ow1


Resolution: 2→41.816 Å / SU ML: 0.53 / σ(F): 0 / Phase error: 20.96 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2232 10558 5.03 %RANDOM
Rwork0.1726 ---
all0.1752 210043 --
obs0.1752 210043 99.97 %-
Solvent computationShrinkage radii: 0.95 Å / VDW probe radii: 1.2 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 45.486 Å2 / ksol: 0.4 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--5.0407 Å20 Å20 Å2
2---0.1538 Å20 Å2
3---5.1945 Å2
Refinement stepCycle: LAST / Resolution: 2→41.816 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms24456 0 118 1921 26495
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00725278
X-RAY DIFFRACTIONf_angle_d1.04934438
X-RAY DIFFRACTIONf_dihedral_angle_d13.319156
X-RAY DIFFRACTIONf_chiral_restr0.0743726
X-RAY DIFFRACTIONf_plane_restr0.0054488
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2-2.02270.30173010.23416586X-RAY DIFFRACTION100
2.0227-2.04650.27983460.21136630X-RAY DIFFRACTION100
2.0465-2.07150.28383330.20666578X-RAY DIFFRACTION100
2.0715-2.09770.26993470.20226612X-RAY DIFFRACTION100
2.0977-2.12530.2583430.18386589X-RAY DIFFRACTION100
2.1253-2.15440.25853360.18486610X-RAY DIFFRACTION100
2.1544-2.18520.2513710.18196535X-RAY DIFFRACTION100
2.1852-2.21780.24353440.17616659X-RAY DIFFRACTION100
2.2178-2.25250.25373250.18426636X-RAY DIFFRACTION100
2.2525-2.28940.23763520.1716595X-RAY DIFFRACTION100
2.2894-2.32890.23633860.17316556X-RAY DIFFRACTION100
2.3289-2.37120.25613670.17816563X-RAY DIFFRACTION100
2.3712-2.41680.2433630.17056609X-RAY DIFFRACTION100
2.4168-2.46610.23693480.16586623X-RAY DIFFRACTION100
2.4661-2.51970.2253750.15926606X-RAY DIFFRACTION100
2.5197-2.57840.23873610.15936574X-RAY DIFFRACTION100
2.5784-2.64280.23383410.16856674X-RAY DIFFRACTION100
2.6428-2.71430.25353510.17466634X-RAY DIFFRACTION100
2.7143-2.79410.23123760.16616598X-RAY DIFFRACTION100
2.7941-2.88430.2333760.16136634X-RAY DIFFRACTION100
2.8843-2.98730.20473170.15526686X-RAY DIFFRACTION100
2.9873-3.10690.22263410.16236643X-RAY DIFFRACTION100
3.1069-3.24830.20173720.15766643X-RAY DIFFRACTION100
3.2483-3.41950.17863700.14926654X-RAY DIFFRACTION100
3.4195-3.63360.19613470.15496703X-RAY DIFFRACTION100
3.6336-3.91390.18253250.15616732X-RAY DIFFRACTION100
3.9139-4.30750.19913670.156708X-RAY DIFFRACTION100
4.3075-4.92990.17053620.15716757X-RAY DIFFRACTION100
4.9299-6.20790.23273510.19396823X-RAY DIFFRACTION100
6.2079-41.82490.24433640.23697035X-RAY DIFFRACTION100
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)
10.48150.0748-0.09360.5085-0.10120.41080.0127-0.13730.0730.1052-0.0124-0.0758-0.04850.0304-0.00230.0807-0.0074-0.0220.1032-0.02670.0623-9.735823.481475.7839
20.57910.039-0.11640.451-0.0720.2743-0.00530.1221-0.0633-0.0705-0.00890.05070.0063-0.06330.01320.0864-0.0027-0.01530.1223-0.03290.072-59.703-8.858947.9275
30.504-0.04450.08370.3933-0.01980.4132-0.0138-0.1180.07250.1168-0.01830.0614-0.0283-0.06180.02880.1142-0.00390.01740.1056-0.03260.0734-54.068217.555476.2904
40.45870.08870.09380.41580.16890.33610.0003-0.0643-0.10170.0606-0.01970.03430.0482-0.05520.01660.0869-0.01760.0280.09560.01930.1019-48.0692-26.652974.0661
50.41130.04050.06230.36810.02220.2234-0.01120.08390.037-0.0686-0.0034-0.0722-0.010.03140.00880.0644-0.00960.02640.06910.02280.05371.13738.268947.8252
60.4032-0.07120.00370.5077-0.05130.2513-0.01750.0739-0.112-0.0559-0.0088-0.02270.0692-0.00780.02020.06810.00110.02640.0646-0.02850.0791-20.845-30.591846.2566
70.5109-0.0246-0.0280.63760.09290.4325-0.01520.06760.1238-0.0789-0.00070.0261-0.0738-0.03050.01360.08590.0005-0.00860.07410.02190.0902-37.712530.190649.7886
80.3356-0.0317-0.08430.2346-0.02520.4798-0.0316-0.114-0.08430.0426-0.0057-0.05270.08550.07520.02670.07560.01-0.00260.08440.03610.0879-3.8004-20.751773.5477
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain A
2X-RAY DIFFRACTION2chain B
3X-RAY DIFFRACTION3chain C
4X-RAY DIFFRACTION4chain D
5X-RAY DIFFRACTION5chain E
6X-RAY DIFFRACTION6chain F
7X-RAY DIFFRACTION7chain G
8X-RAY DIFFRACTION8chain H

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