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- PDB-3qqm: Crystal structure of a Putative amino-acid aminotransferase (NP_1... -

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Basic information

Entry
Database: PDB / ID: 3qqm
TitleCrystal structure of a Putative amino-acid aminotransferase (NP_104211.1) from Mesorhizobium loti at 2.30 A resolution
ComponentsMlr3007 protein
KeywordsTRANSFERASE / STRUCTURAL GENOMICS / JOINT CENTER FOR STRUCTURAL GENOMICS / JCSG / PROTEIN STRUCTURE INITIATIVE / PSI-BIOLOGY
Function / homology
Function and homology information


carboxylic acid biosynthetic process / catalytic activity
Similarity search - Function
Aminotransferase, class IV, conserved site / Aminotransferases class-IV signature. / : / Aminotransferase class 4, branched-chain amino acid transferase, N-terminal domain / D-amino Acid Aminotransferase; Chain A, domain 2 / D-amino Acid Aminotransferase, subunit A, domain 2 / Branched-chain-amino-acid aminotransferase-like, N-terminal / Aminotransferase class IV / Aminotransferase-like, PLP-dependent enzymes / Branched-chain-amino-acid aminotransferase-like, C-terminal ...Aminotransferase, class IV, conserved site / Aminotransferases class-IV signature. / : / Aminotransferase class 4, branched-chain amino acid transferase, N-terminal domain / D-amino Acid Aminotransferase; Chain A, domain 2 / D-amino Acid Aminotransferase, subunit A, domain 2 / Branched-chain-amino-acid aminotransferase-like, N-terminal / Aminotransferase class IV / Aminotransferase-like, PLP-dependent enzymes / Branched-chain-amino-acid aminotransferase-like, C-terminal / Amino-transferase class IV / D-amino Acid Aminotransferase; Chain A, domain 1 / Alpha-Beta Barrel / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
IODIDE ION / DI(HYDROXYETHYL)ETHER / Probable branched-chain-amino-acid aminotransferase
Similarity search - Component
Biological speciesMesorhizobium loti (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.3 Å
AuthorsJoint Center for Structural Genomics (JCSG)
CitationJournal: To be published
Title: Crystal structure of a Putative amino-acid aminotransferase (NP_104211.1) from Mesorhizobium loti at 2.30 A resolution
Authors: Joint Center for Structural Genomics (JCSG)
History
DepositionFeb 15, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 2, 2011Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Jul 20, 2011Group: Structure summary
Revision 1.3Nov 8, 2017Group: Refinement description / Category: software / Item: _software.classification / _software.name

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Mlr3007 protein
B: Mlr3007 protein
C: Mlr3007 protein
D: Mlr3007 protein
E: Mlr3007 protein
F: Mlr3007 protein
G: Mlr3007 protein
H: Mlr3007 protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)204,99399
Polymers197,9878
Non-polymers7,00591
Water13,926773
1
A: Mlr3007 protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,80317
Polymers24,7481
Non-polymers1,05516
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Mlr3007 protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,73512
Polymers24,7481
Non-polymers98611
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: Mlr3007 protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,69012
Polymers24,7481
Non-polymers94211
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
4
D: Mlr3007 protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,94518
Polymers24,7481
Non-polymers1,19617
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
5
E: Mlr3007 protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,66715
Polymers24,7481
Non-polymers91914
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
6
F: Mlr3007 protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,2536
Polymers24,7481
Non-polymers5055
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
7
G: Mlr3007 protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,3518
Polymers24,7481
Non-polymers6027
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
8
H: Mlr3007 protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,54911
Polymers24,7481
Non-polymers80010
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)116.178, 215.574, 81.875
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP21212
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
31C
41D
51E
61F
71G
81H

NCS domain segments:
Dom-IDComponent-IDEns-IDRefine codeAuth asym-IDAuth seq-ID
1114A1 - 220
2114B1 - 220
3114C1 - 220
4114D1 - 220
5114E1 - 220
6114F1 - 220
7114G1 - 220
8114H1 - 220

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Components

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Protein , 1 types, 8 molecules ABCDEFGH

#1: Protein
Mlr3007 protein


Mass: 24748.404 Da / Num. of mol.: 8
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mesorhizobium loti (bacteria) / Gene: mlr3007 / Plasmid: SpeedET / Production host: Escherichia coli (E. coli) / Strain (production host): HK100 / References: UniProt: Q98H69

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Non-polymers , 5 types, 864 molecules

#2: Chemical...
ChemComp-IOD / IODIDE ION


Mass: 126.904 Da / Num. of mol.: 26 / Source method: obtained synthetically / Formula: I
#3: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 14 / Source method: obtained synthetically / Formula: Cl
#4: Chemical...
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 50 / Source method: obtained synthetically / Formula: C2H6O2
#5: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O3
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 773 / Source method: isolated from a natural source / Formula: H2O

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Details

Sequence detailsTHIS CONSTRUCT (RESIDUES 1-220) WAS EXPRESSED WITH A PURIFICATION TAG MGSDKIHHHHHHENLYFQG. THE TAG ...THIS CONSTRUCT (RESIDUES 1-220) WAS EXPRESSED WITH A PURIFICATION TAG MGSDKIHHHHHHENLYFQG. THE TAG WAS REMOVED WITH TEV PROTEASE LEAVING ONLY A GLYCINE (0) 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: 2.59 Å3/Da / Density % sol: 52.49 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 6.2
Details: 0.200M NH4I, 20.00% PEG-3350, No Buffer pH 6.2, NANODROP, VAPOR DIFFUSION, SITTING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL9-2 / Wavelength: 0.97915
DetectorType: MARMOSAIC 325 mm CCD / Detector: CCD / Date: Mar 20, 2009 / Details: FLAT COLLIMATING MIRROR, TOROID FOCUSING MIRROR
RadiationMonochromator: DOUBLE CRYSTAL MONOCHROMATOR SI(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97915 Å / Relative weight: 1
ReflectionResolution: 2.3→29.683 Å / Num. obs: 91682 / % possible obs: 98.6 % / Observed criterion σ(I): -3 / Biso Wilson estimate: 32.589 Å2 / Rmerge(I) obs: 0.084 / Net I/σ(I): 8.97
Reflection shell
Resolution (Å)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. unique obsDiffraction-ID% possible all
2.3-2.380.4281.83155516526196.2
2.38-2.480.3682.13543218456199.1
2.48-2.590.2892.73256716924199
2.59-2.730.2313.53470818000199.2
2.73-2.90.1794.33339617283199
2.9-3.120.1246.33322417167199.1
3.12-3.430.0759.93357017324199
3.43-3.930.04715.63419617612198.7
3.93-4.930.03221.33356417222198.7
4.93-29.6830.031223440917591197.9

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Phasing

PhasingMethod: SAD

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Processing

Software
NameVersionClassificationNB
MolProbity3beta29model building
PDB_EXTRACT3.1data extraction
SHELXDphasing
autoSHARPphasing
XSCALEdata scaling
REFMAC5.5.0110refinement
XDSdata reduction
RefinementMethod to determine structure: SAD / Resolution: 2.3→29.683 Å / Cor.coef. Fo:Fc: 0.936 / Cor.coef. Fo:Fc free: 0.909 / Occupancy max: 1 / Occupancy min: 0.25 / SU B: 11.129 / SU ML: 0.15 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.312 / ESU R Free: 0.228
Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES
Details: 1. HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. 2. ATOM RECORD CONTAINS RESIDUAL B FACTORS ONLY. 3. A MET-INHIBITION PROTOCOL WAS USED FOR SELENOMETHIONINE INCORPORATION DURING PROTEIN ...Details: 1. HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. 2. ATOM RECORD CONTAINS RESIDUAL B FACTORS ONLY. 3. 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 TO ACCOUNT FOR THE REDUCED SCATTERING POWER DUE TO PARTIAL S-MET INCORPORATION. 4. CHLORIDE (CL) AND IODIDE (IOD) IONS FROM THE PURIFICATION AND CRYSTALLIZATION SOLUTIONS HAVE BEEN MODELED INTO THE STRUCTURE. BOTH HALIDES BIND IN SIMILAR ENVIRONMENTS AND MANY OF THE STIES LIKELY CONTAIN A MIXTURE OF I- AND CL- WITH INCOMPLETE OCCUPANCY. OCCUPANCIES WERE ESTIMATED WITH REFINEMENT IN PHENIX.REFINE. IODIDES WERE MODELED AT POSITIONS SUPPORTED BY ANOMALOUS DIFFERENCE FOURIERS PEAKS AND SITES THAT PHENIX.REFINE REFINED OCCUPANCIES GREATER THAN 1.1 WHEN MODELED AS CHLORIDE. 5. ETHYLENE GLYCOL (EDO), USED AS A CRYOPROTECTANT AND POLYETHYLENE GLYCOL (PEG) FROM THE CRYSTALLIZATION SOLUTION WERE MODELED INTO THE STRUCTURE. 6. ELECTRON DENSITY SUPPORTS THE MODELING OF A BOUND PYRIDOXAL-5'-PHOSPHATE (PLP) COFACTOR ON EACH SUBUNIT AS N'-PYRIDOXYL-LYSINE-5'-MONOPHOSPHATE (LLP), IN WHICH THE PLP COFACTOR IS COVALENTLY BOUND TO LYS 117. ANISOU RECORD CONTAINS SUM OF TLS AND RESIDUAL U FACTORS. 8. TLS GROUPS WERE ASSIGNED WITH THE AID OF THE TLSMD SERVER.
RfactorNum. reflection% reflectionSelection details
Rfree0.2407 4592 5 %RANDOM
Rwork0.1932 ---
obs0.1956 91628 99.63 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso max: 60.73 Å2 / Biso mean: 23.3535 Å2 / Biso min: 5.71 Å2
Baniso -1Baniso -2Baniso -3
1-0.71 Å20 Å20 Å2
2---0.37 Å20 Å2
3----0.34 Å2
Refinement stepCycle: LAST / Resolution: 2.3→29.683 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms13129 0 247 773 14149
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.02113611
X-RAY DIFFRACTIONr_bond_other_d0.0010.029442
X-RAY DIFFRACTIONr_angle_refined_deg1.4611.99418388
X-RAY DIFFRACTIONr_angle_other_deg0.803322696
X-RAY DIFFRACTIONr_dihedral_angle_1_deg2.43751708
X-RAY DIFFRACTIONr_dihedral_angle_2_deg27.57722.401629
X-RAY DIFFRACTIONr_dihedral_angle_3_deg9.411152212
X-RAY DIFFRACTIONr_dihedral_angle_4_deg8.54115166
X-RAY DIFFRACTIONr_chiral_restr0.0770.22070
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0215209
X-RAY DIFFRACTIONr_gen_planes_other0.0010.022905
X-RAY DIFFRACTIONr_mcbond_it0.3291.58418
X-RAY DIFFRACTIONr_mcbond_other0.0791.53445
X-RAY DIFFRACTIONr_mcangle_it0.64213383
X-RAY DIFFRACTIONr_scbond_it1.05635193
X-RAY DIFFRACTIONr_scangle_it1.7884.54990
Refine LS restraints NCS

Dom-ID: 1 / Ens-ID: 1 / Number: 2582 / Refine-ID: X-RAY DIFFRACTION

Auth asym-IDTypeRms dev position (Å)Weight position
AMEDIUM POSITIONAL0.450.5
BMEDIUM POSITIONAL0.590.5
CMEDIUM POSITIONAL0.580.5
DMEDIUM POSITIONAL0.460.5
EMEDIUM POSITIONAL0.580.5
FMEDIUM POSITIONAL0.450.5
GMEDIUM POSITIONAL0.510.5
HMEDIUM POSITIONAL0.480.5
AMEDIUM THERMAL0.652
BMEDIUM THERMAL0.592
CMEDIUM THERMAL0.522
DMEDIUM THERMAL0.622
EMEDIUM THERMAL0.522
FMEDIUM THERMAL0.562
GMEDIUM THERMAL0.642
HMEDIUM THERMAL0.52
LS refinement shellResolution: 2.301→2.361 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.297 358 -
Rwork0.246 6268 -
all-6626 -
obs--98.6 %
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)
10.5457-0.02580.03970.5447-0.22881.4067-0.0015-0.01330.01260.03340.02160.0246-0.1128-0.0321-0.02010.01980.00420.01570.0080.00230.0195-34.241944.7338-28.8984
20.2995-0.0786-0.14930.5156-0.52362.89790.01470.0064-0.02680.0225-0.0159-0.0007-0.05730.16980.00110.0418-0.00130.00030.0362-0.0090.0141-25.796743.83139.4693
30.5805-0.1171-0.13270.5432-0.24661.496-0.03060.0371-0.01680.0261-0.0068-0.0247-0.0236-0.0910.03750.03740.0096-0.010.0353-0.01160.0068-43.437475.7145-8.4269
40.6758-0.129-0.12980.69230.16970.76550.04010.01230.0235-0.0123-0.03130.0001-0.0344-0.0012-0.00890.0165-0.0014-0.00680.01090.01250.0168-43.921484.514729.683
50.901-0.2520.18610.7376-0.21410.86280.0003-0.0256-0.00510.00330.0354-0.00820.007-0.0312-0.03570.01230.0017-0.00140.01410.01580.0279-14.008972.408729.3267
61.605-0.1728-0.88620.7001-0.08322.47810.06130.274-0.0517-0.063600.032-0.0283-0.1543-0.06120.04010.0305-0.00160.10480.01320.0616-3.551479.6597-7.6732
70.72040.34110.0611.16410.59831.93250.03420.03340.0758-0.1302-0.01580.115-0.12630.0585-0.01840.1537-0.02670.00210.01730.01270.0812-28.0479111.6893-7.9154
81.0420.294-0.15251.0249-0.17340.79830.011-0.0375-0.0994-0.04790.01510.00060.00180.005-0.02610.01150.0005-0.00880.00140.00150.0641-34.6473121.938529.7729
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A6 - 220
2X-RAY DIFFRACTION2B14 - 220
3X-RAY DIFFRACTION3C12 - 220
4X-RAY DIFFRACTION4D10 - 220
5X-RAY DIFFRACTION5E14 - 220
6X-RAY DIFFRACTION6F6 - 220
7X-RAY DIFFRACTION7G6 - 220
8X-RAY DIFFRACTION8H14 - 220

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