HEADER TRANSFERASE 20-JUL-12 4G78 TITLE SUBATOMIC RESOLUTION CRYSTAL STRUCTURE OF HISTIDINE-CONTAINING TITLE 2 PHOSPHOTRANSFER PROTEIN MTHPT2 FROM MEDICAGO TRUNCATULA COMPND MOL_ID: 1; COMPND 2 MOLECULE: HISTIDINE PHOSPHOTRANSFER PROTEIN; COMPND 3 CHAIN: A; COMPND 4 EC: 2.7.3.-; COMPND 5 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: MEDICAGO TRUNCATULA; SOURCE 3 ORGANISM_COMMON: BARREL MEDIC; SOURCE 4 ORGANISM_TAXID: 3880; SOURCE 5 GENE: MTHPT2, MTR_1G089130, MTR_1G089350; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 511693; SOURCE 8 EXPRESSION_SYSTEM_STRAIN: BL21 MAGIC; SOURCE 9 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 10 EXPRESSION_SYSTEM_PLASMID: PMCSG48 KEYWDS SUBATOMIC RESOLUTION, HELIX BUNDLE, PLANT HORMONE SIGNAL KEYWDS 2 TRANSDUCTION, HISTIDINE KINASE, TRANSFERASE EXPDTA X-RAY DIFFRACTION AUTHOR M.RUSZKOWSKI,M.SIKORSKI,M.JASKOLSKI REVDAT 2 13-SEP-23 4G78 1 SEQADV REVDAT 1 24-JUL-13 4G78 0 JRNL AUTH M.RUSZKOWSKI,M.SIKORSKI,M.JASKOLSKI JRNL TITL SUBATOMIC RESOLUTION CRYSTAL STRUCTURE OF JRNL TITL 2 HISTIDINE-CONTAINING PHOSPHOTRANSFER PROTEIN MTHPT2 FROM JRNL TITL 3 MEDICAGO TRUNCATULA JRNL REF TO BE PUBLISHED JRNL REFN REMARK 1 REMARK 1 REFERENCE 1 REMARK 1 AUTH C.E.HUTCHISON,J.LI,C.ARGUESO,M.GONZALEZ,E.LEE,M.W.LEWIS, REMARK 1 AUTH 2 B.B.MAXWELL,T.D.PERDUE,G.E.SCHALLER,J.M.ALONSO,J.R.ECKER, REMARK 1 AUTH 3 J.J.KIEBER REMARK 1 TITL THE ARABIDOPSIS HISTIDINE PHOSPHOTRANSFER PROTEINS ARE REMARK 1 TITL 2 REDUNDANT POSITIVE REGULATORS OF CYTOKININ SIGNALING. REMARK 1 REF PLANT CELL V. 18 3073 2006 REMARK 1 REFN ISSN 1040-4651 REMARK 1 PMID 17122069 REMARK 1 DOI 10.1105/TPC.106.045674 REMARK 1 REFERENCE 2 REMARK 1 AUTH H.SUGAWARA,Y.KAWANO,T.HATAKEYAMA,T.YAMAYA,N.KAMIYA, REMARK 1 AUTH 2 H.SAKAKIBARA REMARK 1 TITL CRYSTAL STRUCTURE OF THE HISTIDINE-CONTAINING REMARK 1 TITL 2 PHOSPHOTRANSFER PROTEIN ZMHP2 FROM MAIZE. REMARK 1 REF PROTEIN SCI. V. 14 202 2005 REMARK 1 REFN ISSN 0961-8368 REMARK 1 PMID 15576555 REMARK 1 DOI 10.1110/PS.041076905 REMARK 1 REFERENCE 3 REMARK 1 AUTH Q.XU,A.H.WEST REMARK 1 TITL CONSERVATION OF STRUCTURE AND FUNCTION AMONG REMARK 1 TITL 2 HISTIDINE-CONTAINING PHOSPHOTRANSFER (HPT) DOMAINS AS REMARK 1 TITL 3 REVEALED BY THE CRYSTAL STRUCTURE OF YPD1. REMARK 1 REF J.MOL.BIOL. V. 292 1039 1999 REMARK 1 REFN ISSN 0022-2836 REMARK 1 PMID 10512701 REMARK 1 DOI 10.1006/JMBI.1999.3143 REMARK 2 REMARK 2 RESOLUTION. 0.92 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : SHELX REMARK 3 AUTHORS : G.M.SHELDRICK REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 0.92 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 50.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 97.8 REMARK 3 CROSS-VALIDATION METHOD : R-FREE REMARK 3 FREE R VALUE TEST SET SELECTION : RAMDOM REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT (NO CUTOFF). REMARK 3 R VALUE (WORKING + TEST SET, NO CUTOFF) : NULL REMARK 3 R VALUE (WORKING SET, NO CUTOFF) : 0.121 REMARK 3 FREE R VALUE (NO CUTOFF) : 0.155 REMARK 3 FREE R VALUE TEST SET SIZE (%, NO CUTOFF) : NULL REMARK 3 FREE R VALUE TEST SET COUNT (NO CUTOFF) : 1008 REMARK 3 TOTAL NUMBER OF REFLECTIONS (NO CUTOFF) : 84634 REMARK 3 REMARK 3 FIT/AGREEMENT OF MODEL FOR DATA WITH F>4SIG(F). REMARK 3 R VALUE (WORKING + TEST SET, F>4SIG(F)) : 0.110 REMARK 3 R VALUE (WORKING SET, F>4SIG(F)) : 0.110 REMARK 3 FREE R VALUE (F>4SIG(F)) : 0.144 REMARK 3 FREE R VALUE TEST SET SIZE (%, F>4SIG(F)) : NULL REMARK 3 FREE R VALUE TEST SET COUNT (F>4SIG(F)) : 800 REMARK 3 TOTAL NUMBER OF REFLECTIONS (F>4SIG(F)) : 67864 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 1182 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 0 REMARK 3 SOLVENT ATOMS : 207 REMARK 3 REMARK 3 MODEL REFINEMENT. REMARK 3 OCCUPANCY SUM OF NON-HYDROGEN ATOMS : NULL REMARK 3 OCCUPANCY SUM OF HYDROGEN ATOMS : NULL REMARK 3 NUMBER OF DISCRETELY DISORDERED RESIDUES : NULL REMARK 3 NUMBER OF LEAST-SQUARES PARAMETERS : NULL REMARK 3 NUMBER OF RESTRAINTS : NULL REMARK 3 REMARK 3 RMS DEVIATIONS FROM RESTRAINT TARGET VALUES. REMARK 3 BOND LENGTHS (A) : 0.023 REMARK 3 ANGLE DISTANCES (A) : 0.040 REMARK 3 SIMILAR DISTANCES (NO TARGET VALUES) (A) : NULL REMARK 3 DISTANCES FROM RESTRAINT PLANES (A) : 0.300 REMARK 3 ZERO CHIRAL VOLUMES (A**3) : NULL REMARK 3 NON-ZERO CHIRAL VOLUMES (A**3) : 0.157 REMARK 3 ANTI-BUMPING DISTANCE RESTRAINTS (A) : NULL REMARK 3 RIGID-BOND ADP COMPONENTS (A**2) : NULL REMARK 3 SIMILAR ADP COMPONENTS (A**2) : NULL REMARK 3 APPROXIMATELY ISOTROPIC ADPS (A**2) : NULL REMARK 3 REMARK 3 BULK SOLVENT MODELING. REMARK 3 METHOD USED: BABINET MODEL REMARK 3 REMARK 3 STEREOCHEMISTRY TARGET VALUES : ENGH & HUBER REMARK 3 SPECIAL CASE: NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: HYDROGEN ATOMS WERE ADDED AT RIDING REMARK 3 POSITIONS REMARK 4 REMARK 4 4G78 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 24-JUL-12. REMARK 100 THE DEPOSITION ID IS D_1000073825. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 17-MAR-12 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 6.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : BESSY REMARK 200 BEAMLINE : 14.2 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.91841 REMARK 200 MONOCHROMATOR : SAGITALLY FOCUSED SI(111) REMARK 200 OPTICS : FOCUSING MIRRORS REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : MARMOSAIC 225 MM CCD REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : XSCALE REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 84634 REMARK 200 RESOLUTION RANGE HIGH (A) : 0.920 REMARK 200 RESOLUTION RANGE LOW (A) : 50.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : -3.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 97.8 REMARK 200 DATA REDUNDANCY : 6.300 REMARK 200 R MERGE (I) : 0.03600 REMARK 200 R SYM (I) : NULL REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 21.7800 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 0.92 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 0.94 REMARK 200 COMPLETENESS FOR SHELL (%) : 75.1 REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : 0.73800 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 <I/SIGMA(I)> FOR SHELL : 1.890 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: PHASER REMARK 200 STARTING MODEL: PDB ENTRY 3US6 REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 32.01 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 1.81 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.09M HALOGENS, 0.1M BUFFER SYSTEM 1, REMARK 280 30% PEG 550MME + PEG 20K (MOLECULAR DIMENSIONS MORPHEUS SCREEN REMARK 280 B1), PH 6.5, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 292K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 1 21 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,Y+1/2,-Z REMARK 290 REMARK 290 WHERE NNN -> OPERATOR NUMBER REMARK 290 MMM -> TRANSLATION VECTOR REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY TRANSFORMATIONS REMARK 290 THE FOLLOWING TRANSFORMATIONS OPERATE ON THE ATOM/HETATM REMARK 290 RECORDS IN THIS ENTRY TO PRODUCE CRYSTALLOGRAPHICALLY REMARK 290 RELATED MOLECULES. REMARK 290 SMTRY1 1 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 1 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 1 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 2 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 2 0.000000 1.000000 0.000000 25.07500 REMARK 290 SMTRY3 2 0.000000 0.000000 -1.000000 0.00000 REMARK 290 REMARK 290 REMARK: NULL REMARK 300 REMARK 300 BIOMOLECULE: 1 REMARK 300 SEE REMARK 350 FOR THE AUTHOR PROVIDED AND/OR PROGRAM REMARK 300 GENERATED ASSEMBLY INFORMATION FOR THE STRUCTURE IN REMARK 300 THIS ENTRY. THE REMARK MAY ALSO PROVIDE INFORMATION ON REMARK 300 BURIED SURFACE AREA. REMARK 350 REMARK 350 COORDINATES FOR A COMPLETE MULTIMER REPRESENTING THE KNOWN REMARK 350 BIOLOGICALLY SIGNIFICANT OLIGOMERIZATION STATE OF THE REMARK 350 MOLECULE CAN BE GENERATED BY APPLYING BIOMT TRANSFORMATIONS REMARK 350 GIVEN BELOW. BOTH NON-CRYSTALLOGRAPHIC AND REMARK 350 CRYSTALLOGRAPHIC OPERATIONS ARE GIVEN. REMARK 350 REMARK 350 BIOMOLECULE: 1 REMARK 350 AUTHOR DETERMINED BIOLOGICAL UNIT: MONOMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: MONOMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 APPLY THE FOLLOWING TO CHAINS: A REMARK 350 BIOMT1 1 1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT2 1 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT3 1 0.000000 0.000000 1.000000 0.00000 REMARK 465 REMARK 465 MISSING RESIDUES REMARK 465 THE FOLLOWING RESIDUES WERE NOT LOCATED IN THE REMARK 465 EXPERIMENT. (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 465 IDENTIFIER; SSSEQ=SEQUENCE NUMBER; I=INSERTION CODE.) REMARK 465 REMARK 465 M RES C SSSEQI REMARK 465 ILE A 145 REMARK 465 HIS A 146 REMARK 465 THR A 147 REMARK 465 ARG A 148 REMARK 465 GLY A 149 REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: COVALENT BOND LENGTHS REMARK 500 REMARK 500 THE STEREOCHEMICAL PARAMETERS OF THE FOLLOWING RESIDUES REMARK 500 HAVE VALUES WHICH DEVIATE FROM EXPECTED VALUES BY MORE REMARK 500 THAN 6*RMSD (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 500 IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 STANDARD TABLE: REMARK 500 FORMAT: (10X,I3,1X,2(A3,1X,A1,I4,A1,1X,A4,3X),1X,F6.3) REMARK 500 REMARK 500 EXPECTED VALUES PROTEIN: ENGH AND HUBER, 1999 REMARK 500 EXPECTED VALUES NUCLEIC ACID: CLOWNEY ET AL 1996 REMARK 500 REMARK 500 M RES CSSEQI ATM1 RES CSSEQI ATM2 DEVIATION REMARK 500 CYS A 110 CB CYS A 110 SG -0.150 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: COVALENT BOND ANGLES REMARK 500 REMARK 500 THE STEREOCHEMICAL PARAMETERS OF THE FOLLOWING RESIDUES REMARK 500 HAVE VALUES WHICH DEVIATE FROM EXPECTED VALUES BY MORE REMARK 500 THAN 6*RMSD (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 500 IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 STANDARD TABLE: REMARK 500 FORMAT: (10X,I3,1X,A3,1X,A1,I4,A1,3(1X,A4,2X),12X,F5.1) REMARK 500 REMARK 500 EXPECTED VALUES PROTEIN: ENGH AND HUBER, 1999 REMARK 500 EXPECTED VALUES NUCLEIC ACID: CLOWNEY ET AL 1996 REMARK 500 REMARK 500 M RES CSSEQI ATM1 ATM2 ATM3 REMARK 500 SER A 36 O - C - N ANGL. DEV. = -11.6 DEGREES REMARK 500 SER A 36 O - C - N ANGL. DEV. = 20.3 DEGREES REMARK 500 PRO A 37 C - N - CA ANGL. DEV. = 10.0 DEGREES REMARK 500 PHE A 39 C - N - CA ANGL. DEV. = 17.4 DEGREES REMARK 500 ASP A 73 CB - CG - OD1 ANGL. DEV. = 10.0 DEGREES REMARK 500 ASP A 73 CB - CG - OD2 ANGL. DEV. = -11.5 DEGREES REMARK 500 CYS A 110 CA - CB - SG ANGL. DEV. = -13.9 DEGREES REMARK 500 GLN A 119 CG - CD - OE1 ANGL. DEV. = 14.8 DEGREES REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: MAIN CHAIN PLANARITY REMARK 500 REMARK 500 THE FOLLOWING RESIDUES HAVE A PSEUDO PLANARITY REMARK 500 TORSION ANGLE, C(I) - CA(I) - N(I+1) - O(I), GREATER REMARK 500 10.0 DEGREES. (M=MODEL NUMBER; RES=RESIDUE NAME; REMARK 500 C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; REMARK 500 I=INSERTION CODE). REMARK 500 REMARK 500 M RES CSSEQI ANGLE REMARK 500 SER A 36 -10.00 REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 3US6 RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF HISTIDINE-CONTAINING PHOSPHOTRANSFER PROTEIN REMARK 900 MTHPT1 FROM MEDICAGO TRUNCATULA REMARK 900 RELATED ID: 1YVI RELATED DB: PDB REMARK 900 X-RAY STRUCTURE OF PUTATIVE HISTIDINE-CONTAINING PHOSPHOTRANSFER REMARK 900 PROTEIN FROM RICE, AK104879 REMARK 900 RELATED ID: 2Q4F RELATED DB: PDB REMARK 900 ENSEMBLE REFINEMENT OF THE CRYSTAL STRUCTURE OF PUTATIVE HISTIDINE- REMARK 900 CONTAINING PHOSPHOTRANSFER PROTEIN FROM RICE, AK104879 REMARK 900 RELATED ID: 1WN0 RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF HISTIDINE-CONTAINING PHOSPHOTRANSFER PROTEIN, REMARK 900 ZMHP2, FROM MAIZE REMARK 900 RELATED ID: 1QSP RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF THE YEAST PHOSPHORELAY PROTEIN YPD1 DBREF 4G78 A 1 149 UNP G7I2T8 G7I2T8_MEDTR 1 149 SEQADV 4G78 SER A -2 UNP G7I2T8 EXPRESSION TAG SEQADV 4G78 ASN A -1 UNP G7I2T8 EXPRESSION TAG SEQADV 4G78 ALA A 0 UNP G7I2T8 EXPRESSION TAG SEQRES 1 A 152 SER ASN ALA MET ASP HIS LEU HIS ARG LYS LEU ARG ASP SEQRES 2 A 152 HIS GLU ALA ALA MET PHE GLN GLN GLY TYR LEU ASP ASP SEQRES 3 A 152 GLN PHE SER GLN LEU GLN LYS LEU GLN ASP ASP THR SER SEQRES 4 A 152 PRO ASP PHE VAL ILE GLU VAL MET THR MET PHE PHE ASP SEQRES 5 A 152 ASP SER GLU LYS LEU LEU ASN ASN MET SER ARG ALA LEU SEQRES 6 A 152 GLU GLN VAL PRO VAL ASN PHE LYS GLN ILE ASP ALA HIS SEQRES 7 A 152 ALA HIS GLN GLN LYS GLY SER SER ALA SER VAL GLY ALA SEQRES 8 A 152 ALA ARG VAL LYS ASN VAL CYS GLY THR PHE ARG ASN PHE SEQRES 9 A 152 CYS GLU ALA GLN ASN LEU GLU GLY CYS VAL ARG CYS LEU SEQRES 10 A 152 GLN GLN LEU GLN GLN GLU TYR SER LEU LEU LYS ASN ASN SEQRES 11 A 152 LEU LYS TYR LEU PHE LYS LEU GLN GLN GLU ILE LYS THR SEQRES 12 A 152 ALA GLY ARG SER ILE HIS THR ARG GLY FORMUL 2 HOH *207(H2 O) HELIX 1 1 ASP A 2 GLN A 18 1 17 HELIX 2 2 ASP A 22 LYS A 30 1 9 HELIX 3 3 PRO A 37 GLN A 64 1 28 HELIX 4 4 ASN A 68 VAL A 86 1 19 HELIX 5 5 ALA A 88 THR A 97 1 10 HELIX 6 6 THR A 97 ALA A 104 1 8 HELIX 7 7 ASN A 106 ARG A 143 1 38 CISPEP 1 VAL A 65 PRO A 66 0 -5.85 CISPEP 2 VAL A 65 PRO A 66 0 -6.87 CISPEP 3 ARG A 143 SER A 144 0 6.65 CRYST1 25.240 50.150 50.380 90.00 97.44 90.00 P 1 21 1 2 ORIGX1 1.000000 0.000000 0.000000 0.00000 ORIGX2 0.000000 1.000000 0.000000 0.00000 ORIGX3 0.000000 0.000000 1.000000 0.00000 SCALE1 0.039620 0.000000 0.005174 0.00000 SCALE2 0.000000 0.019940 0.000000 0.00000 SCALE3 0.000000 0.000000 0.020018 0.00000