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- PDB-2pr7: Crystal structure of uncharacterized protein (NP_599989.1) from C... -

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Entry
Database: PDB / ID: 2pr7
TitleCrystal structure of uncharacterized protein (NP_599989.1) from Corynebacterium glutamicum ATCC 13032 Kitasato at 1.44 A resolution
ComponentsHaloacid dehalogenase/epoxide hydrolase family
KeywordsHYDROLASE / NP_599989.1 / uncharacterized protein / Structural Genomics / Joint Center for Structural Genomics / JCSG / Protein Structure Initiative / PSI-2
Function / homologyHAD superfamily/HAD-like / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta / :
Function and homology information
Biological speciesCorynebacterium glutamicum ATCC 13032 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.44 Å
AuthorsJoint Center for Structural Genomics (JCSG)
CitationJournal: To be published
Title: Crystal structure of uncharacterized protein (NP_599989.1) from Corynebacterium glutamicum ATCC 13032 Kitasato at 1.44 A resolution
Authors: Joint Center for Structural Genomics (JCSG)
History
DepositionMay 3, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 15, 2007Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.3Oct 18, 2017Group: Refinement description / Category: software / Item: _software.classification / _software.name
Revision 1.4Jan 25, 2023Group: Database references / Derived calculations
Category: database_2 / pdbx_struct_conn_angle ...database_2 / pdbx_struct_conn_angle / struct_conn / struct_conn_type / 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_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.conn_type_id / _struct_conn.id / _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_conn.ptnr2_label_seq_id / _struct_conn_type.id / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Remark 999 SEQUENCE THE CONSTRUCT WAS EXPRESSED WITH A PURIFICATION TAG MGSDKIHHHHHHENLYFQG. THE TAG WAS ... SEQUENCE THE CONSTRUCT 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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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Haloacid dehalogenase/epoxide hydrolase family
B: Haloacid dehalogenase/epoxide hydrolase family
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,5097
Polymers29,2422
Non-polymers2665
Water4,828268
1
A: Haloacid dehalogenase/epoxide hydrolase family
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,7854
Polymers14,6211
Non-polymers1643
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Haloacid dehalogenase/epoxide hydrolase family
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,7233
Polymers14,6211
Non-polymers1022
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)29.149, 45.153, 60.777
Angle α, β, γ (deg.)100.720, 103.860, 103.310
Int Tables number1
Space group name H-MP1
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B

NCS domain segments:

Component-ID: 1 / Ens-ID: 1 / Beg label comp-ID: GLY / End label comp-ID: GLU / Refine code: 2 / Auth seq-ID: 0 - 133 / Label seq-ID: 1 - 134

Dom-IDAuth asym-IDLabel asym-ID
1AA
2BB

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Components

#1: Protein Haloacid dehalogenase/epoxide hydrolase family


Mass: 14621.169 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Corynebacterium glutamicum ATCC 13032 (bacteria)
Species: Corynebacterium glutamicum / Strain: DSM 20300, JCM 1318, LMG 3730, NCIMB 10025 / Gene: NP_599989.1, cg0870 / Plasmid: speedET / Production host: Escherichia coli (E. coli) / Strain (production host): HK100 / References: UniProt: Q6M720
#2: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ca
#3: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C2H6O2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 268 / 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: 2.5 Å3/Da / Density % sol: 50.76 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 5.5
Details: NANODROP, 10.0% 2-propanol, 0.3M Calcium acetate, 0.1M MES pH 5.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL11-1 / Wavelength: 0.91162, 0.97929
DetectorType: MARMOSAIC 325 mm CCD / Detector: CCD / Date: Apr 7, 2007 / Details: Flat mirror (vertical focusing)
RadiationMonochromator: Single crystal Si(111) bent (horizontal focusing)
Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.911621
20.979291
ReflectionResolution: 1.44→39.193 Å / Num. obs: 40271 / % possible obs: 77.4 % / Biso Wilson estimate: 25.909 Å2 / Rmerge(I) obs: 0.036 / Net I/σ(I): 14.96
Reflection shell

Diffraction-ID: 1

Resolution (Å)Highest resolution (Å)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. unique all% possible all
1.44-1.490.4672.23810135527.2
1.49-1.550.36235952203039
1.55-1.620.273.98354284755.7
1.62-1.710.2015.213321449882.9
1.71-1.810.1496.913315444893.2
1.81-1.950.08810.814593489194.2
1.95-2.150.05516.114803496695.2
2.15-2.460.03921.914552489295.2
2.460.03226.214540491895.9

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Phasing

PhasingMethod: MAD

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Processing

Software
NameVersionClassificationNB
MolProbity3beta29model building
SHELXphasing
REFMAC5.2.0019refinement
XSCALEdata scaling
PDB_EXTRACT2data extraction
MAR345CCDdata collection
XDSdata reduction
SHELXDphasing
autoSHARPphasing
RefinementMethod to determine structure: MAD / Resolution: 1.44→39.193 Å / Cor.coef. Fo:Fc: 0.973 / Cor.coef. Fo:Fc free: 0.959 / SU B: 3.311 / SU ML: 0.059 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.077 / ESU R Free: 0.079
Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES
Details: 1. HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. 2. A MET-INHIBITION PROTOCOL WAS USED FOR SELENOMETHIONINE INCORPORATION DURING PROTEIN EXPRESSION. THE OCCUPANCY OF THE SE ATOMS IN THE ...Details: 1. HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. 2. A MET-INHIBITION PROTOCOL WAS USED FOR SELENOMETHIONINE INCORPORATION DURING PROTEIN EXPRESSION. THE OCCUPANCY OF THE SE ATOMS IN THE MSE RESIDUES WAS REDUCED TO 0.75 FOR THE REDUCED SCATTERING POWER DUE TO PARTIAL S-MET INCORPORATION. 3. ATOM RECORD CONTAINS RESIDUAL B FACTORS ONLY. 4. CALCIUM IS MODELED BASED ON CRYSTALLIZATION CONDITIONS AND COORDINATION ENVIRONMENT AND GEOMETRY. THE OCCUPANCIES ARE SET AS 0.5 ACCORDING TO DENSITY. STRUCTURAL HOMOLOGS CONTAIN MAGNESIUM AT THE CORRESPONDING SITES. 5. EDO MOLECULES ARE FROM CRYOPROTECTANT. 6. THE NOMINAL RESOLUTION IS 1.60 A WITH 5615 OBSERVED REFLECTIONS BETWEEN 1.60-1.44 (40.5% COMPLETE FOR THIS SHELL) INCLUDED IN THE REFINEMENT.
RfactorNum. reflection% reflectionSelection details
Rfree0.199 2034 5.1 %RANDOM
Rwork0.168 ---
all0.17 ---
obs0.17 40270 78.61 %-
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: 18.534 Å2
Baniso -1Baniso -2Baniso -3
1--0.3 Å20.56 Å2-0.36 Å2
2--1.94 Å2-0.04 Å2
3----1.57 Å2
Refinement stepCycle: LAST / Resolution: 1.44→39.193 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2022 0 14 268 2304
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0170.0222127
X-RAY DIFFRACTIONr_bond_other_d0.0020.021410
X-RAY DIFFRACTIONr_angle_refined_deg1.5431.9862901
X-RAY DIFFRACTIONr_angle_other_deg0.9633455
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.8715295
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.10124.68194
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.74515348
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.7971517
X-RAY DIFFRACTIONr_chiral_restr0.0840.2341
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.022464
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02419
X-RAY DIFFRACTIONr_nbd_refined0.2140.2412
X-RAY DIFFRACTIONr_nbd_other0.2050.21525
X-RAY DIFFRACTIONr_nbtor_refined0.1750.21080
X-RAY DIFFRACTIONr_nbtor_other0.0860.21163
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1970.2158
X-RAY DIFFRACTIONr_metal_ion_refined0.1070.27
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1240.211
X-RAY DIFFRACTIONr_symmetry_vdw_other0.3010.269
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2340.225
X-RAY DIFFRACTIONr_mcbond_it1.96631437
X-RAY DIFFRACTIONr_mcbond_other0.5293586
X-RAY DIFFRACTIONr_mcangle_it2.69452210
X-RAY DIFFRACTIONr_scbond_it4.7818788
X-RAY DIFFRACTIONr_scangle_it6.73811678
Refine LS restraints NCS

Dom-ID: 1 / Auth asym-ID: A / Ens-ID: 1 / Refine-ID: X-RAY DIFFRACTION

NumberTypeRms dev position (Å)Weight position
774TIGHT POSITIONAL0.060.1
795MEDIUM POSITIONAL0.330.5
774TIGHT THERMAL0.320.5
795MEDIUM THERMAL1.082
LS refinement shellResolution: 1.44→1.478 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.327 47 -
Rwork0.313 979 -
obs-1026 27.19 %
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)
11.196-0.05640.40471.23890.57671.71940.00110.13890.04170.0557-0.0192-0.09290.1030.00380.0181-0.0393-0.01670.0068-0.05380.00290.00224.10811.8883.857
21.681-0.0744-0.22141.00490.52472.1714-0.0017-0.0964-0.0087-0.0459-0.0202-0.0678-0.09040.10050.0219-0.02030.018-0.0037-0.07130.0063-0.01169.529-3.10525.45
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION / Selection: ALL / Auth seq-ID: 0 - 136 / Label seq-ID: 1 - 137

IDRefine TLS-IDAuth asym-IDLabel asym-ID
11AA
22BB

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