HEADER TRANSFERASE 08-MAY-12 4F2L
TITLE STRUCTURE OF A REGULATORY DOMAIN OF AMPK
COMPND MOL_ID: 1;
COMPND 2 MOLECULE: 5'-AMP-ACTIVATED PROTEIN KINASE CATALYTIC SUBUNIT ALPHA-1;
COMPND 3 CHAIN: A;
COMPND 4 FRAGMENT: REGULATORY DOMAIN, UNP RESIDUES 295-347;
COMPND 5 SYNONYM: AMPK SUBUNIT ALPHA-1, TAU-PROTEIN KINASE PRKAA1;
COMPND 6 EC: 2.7.11.1, 2.7.11.26;
COMPND 7 ENGINEERED: YES
SOURCE MOL_ID: 1;
SOURCE 2 ORGANISM_SCIENTIFIC: RATTUS NORVEGICUS;
SOURCE 3 ORGANISM_COMMON: BROWN RAT,RAT,RATS;
SOURCE 4 ORGANISM_TAXID: 10116;
SOURCE 5 GENE: PRKAA1, AMPK1;
SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI;
SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562;
SOURCE 8 EXPRESSION_SYSTEM_STRAIN: BL21(DE3);
SOURCE 9 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID;
SOURCE 10 EXPRESSION_SYSTEM_PLASMID: PET21B
KEYWDS REGULATORY DOMAIN, HELIX, AMPK INTRAMOLECULAR INTERACTION,
KEYWDS 2 TRANSFERASE
EXPDTA X-RAY DIFFRACTION
AUTHOR F.J.XIN,Y.Y.ZHANG,J.WANG,Z.X.WANG,J.W.WU
REVDAT 3 15-NOV-17 4F2L 1 REMARK
REVDAT 2 03-SEP-14 4F2L 1 JRNL
REVDAT 1 26-JUN-13 4F2L 0
JRNL AUTH L.CHEN,F.J.XIN,J.WANG,J.HU,Y.Y.ZHANG,S.WAN,L.S.CAO,C.LU,
JRNL AUTH 2 P.LI,S.F.YAN,D.NEUMANN,U.SCHLATTNER,B.XIA,Z.X.WANG,J.W.WU
JRNL TITL CONSERVED REGULATORY ELEMENTS IN AMPK
JRNL REF NATURE V. 498 E8 2013
JRNL REFN ISSN 0028-0836
JRNL PMID 23765502
JRNL DOI 10.1038/NATURE12189
REMARK 2
REMARK 2 RESOLUTION. 1.50 ANGSTROMS.
REMARK 3
REMARK 3 REFINEMENT.
REMARK 3 PROGRAM : PHENIX (PHENIX.REFINE: 1.7.3_928)
REMARK 3 AUTHORS : PAUL ADAMS,PAVEL AFONINE,VINCENT CHEN,IAN
REMARK 3 : DAVIS,KRESHNA GOPAL,RALF GROSSE-KUNSTLEVE,
REMARK 3 : LI-WEI HUNG,ROBERT IMMORMINO,TOM IOERGER,
REMARK 3 : AIRLIE MCCOY,ERIK MCKEE,NIGEL MORIARTY,
REMARK 3 : REETAL PAI,RANDY READ,JANE RICHARDSON,
REMARK 3 : DAVID RICHARDSON,TOD ROMO,JIM SACCHETTINI,
REMARK 3 : NICHOLAS SAUTER,JACOB SMITH,LAURENT
REMARK 3 : STORONI,TOM TERWILLIGER,PETER ZWART
REMARK 3
REMARK 3 REFINEMENT TARGET : ML
REMARK 3
REMARK 3 DATA USED IN REFINEMENT.
REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.50
REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 24.37
REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.900
REMARK 3 COMPLETENESS FOR RANGE (%) : 99.5
REMARK 3 NUMBER OF REFLECTIONS : 24447
REMARK 3
REMARK 3 FIT TO DATA USED IN REFINEMENT.
REMARK 3 R VALUE (WORKING + TEST SET) : 0.183
REMARK 3 R VALUE (WORKING SET) : 0.182
REMARK 3 FREE R VALUE : 0.212
REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.900
REMARK 3 FREE R VALUE TEST SET COUNT : 1198
REMARK 3
REMARK 3 FIT TO DATA USED IN REFINEMENT (IN BINS).
REMARK 3 BIN RESOLUTION RANGE COMPL. NWORK NFREE RWORK RFREE
REMARK 3 1 24.3753 - 3.1183 0.98 2568 108 0.1820 0.2227
REMARK 3 2 3.1183 - 2.4759 0.99 2554 141 0.1820 0.2205
REMARK 3 3 2.4759 - 2.1631 1.00 2595 147 0.1755 0.1780
REMARK 3 4 2.1631 - 1.9655 1.00 2600 128 0.1796 0.1985
REMARK 3 5 1.9655 - 1.8246 1.00 2633 91 0.1682 0.2349
REMARK 3 6 1.8246 - 1.7171 1.00 2575 138 0.1833 0.2231
REMARK 3 7 1.7171 - 1.6311 1.00 2559 163 0.1784 0.1928
REMARK 3 8 1.6311 - 1.5601 1.00 2603 132 0.1987 0.2332
REMARK 3 9 1.5601 - 1.5001 0.99 2562 150 0.2275 0.2470
REMARK 3
REMARK 3 BULK SOLVENT MODELLING.
REMARK 3 METHOD USED : FLAT BULK SOLVENT MODEL
REMARK 3 SOLVENT RADIUS : 1.00
REMARK 3 SHRINKAGE RADIUS : 0.73
REMARK 3 K_SOL : 0.39
REMARK 3 B_SOL : 42.76
REMARK 3
REMARK 3 ERROR ESTIMATES.
REMARK 3 COORDINATE ERROR (MAXIMUM-LIKELIHOOD BASED) : 0.180
REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 17.550
REMARK 3
REMARK 3 B VALUES.
REMARK 3 FROM WILSON PLOT (A**2) : NULL
REMARK 3 MEAN B VALUE (OVERALL, A**2) : NULL
REMARK 3 OVERALL ANISOTROPIC B VALUE.
REMARK 3 B11 (A**2) : -1.63310
REMARK 3 B22 (A**2) : 5.90660
REMARK 3 B33 (A**2) : -4.27350
REMARK 3 B12 (A**2) : 0.00000
REMARK 3 B13 (A**2) : 0.00000
REMARK 3 B23 (A**2) : 0.00000
REMARK 3
REMARK 3 TWINNING INFORMATION.
REMARK 3 FRACTION: NULL
REMARK 3 OPERATOR: NULL
REMARK 3
REMARK 3 DEVIATIONS FROM IDEAL VALUES.
REMARK 3 RMSD COUNT
REMARK 3 BOND : 0.005 538
REMARK 3 ANGLE : 0.902 730
REMARK 3 CHIRALITY : 0.068 78
REMARK 3 PLANARITY : 0.003 98
REMARK 3 DIHEDRAL : 15.646 207
REMARK 3
REMARK 3 TLS DETAILS
REMARK 3 NUMBER OF TLS GROUPS : NULL
REMARK 3
REMARK 3 NCS DETAILS
REMARK 3 NUMBER OF NCS GROUPS : NULL
REMARK 3
REMARK 3 OTHER REFINEMENT REMARKS: THE ENTRY CONTAINS FRIEDEL PAIRS IN
REMARK 3 F_PLUS/MINUS COLUMNS
REMARK 4
REMARK 4 4F2L COMPLIES WITH FORMAT V. 3.30, 13-JUL-11
REMARK 100
REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 18-MAY-12.
REMARK 100 THE DEPOSITION ID IS D_1000072375.
REMARK 200
REMARK 200 EXPERIMENTAL DETAILS
REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION
REMARK 200 DATE OF DATA COLLECTION : 26-MAY-11
REMARK 200 TEMPERATURE (KELVIN) : 100
REMARK 200 PH : 7.5
REMARK 200 NUMBER OF CRYSTALS USED : 1
REMARK 200
REMARK 200 SYNCHROTRON (Y/N) : Y
REMARK 200 RADIATION SOURCE : SSRF
REMARK 200 BEAMLINE : BL17U
REMARK 200 X-RAY GENERATOR MODEL : NULL
REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M
REMARK 200 WAVELENGTH OR RANGE (A) : 0.9792
REMARK 200 MONOCHROMATOR : GRAPHITE
REMARK 200 OPTICS : NULL
REMARK 200
REMARK 200 DETECTOR TYPE : CCD
REMARK 200 DETECTOR MANUFACTURER : MARMOSAIC 225 MM CCD
REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000
REMARK 200 DATA SCALING SOFTWARE : HKL-2000
REMARK 200
REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 24489
REMARK 200 RESOLUTION RANGE HIGH (A) : 1.500
REMARK 200 RESOLUTION RANGE LOW (A) : 50.000
REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 0.000
REMARK 200
REMARK 200 OVERALL.
REMARK 200 COMPLETENESS FOR RANGE (%) : 99.5
REMARK 200 DATA REDUNDANCY : 3.600
REMARK 200 R MERGE (I) : 0.04600
REMARK 200 R SYM (I) : NULL
REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 36.4000
REMARK 200
REMARK 200 IN THE HIGHEST RESOLUTION SHELL.
REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.50
REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.53
REMARK 200 COMPLETENESS FOR SHELL (%) : 98.5
REMARK 200 DATA REDUNDANCY IN SHELL : 3.10
REMARK 200 R MERGE FOR SHELL (I) : 0.26300
REMARK 200 R SYM FOR SHELL (I) : NULL
REMARK 200 <I/SIGMA(I)> FOR SHELL : 3.600
REMARK 200
REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH
REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: NULL
REMARK 200 SOFTWARE USED: AUTOSOL
REMARK 200 STARTING MODEL: NULL
REMARK 200
REMARK 200 REMARK: THE ENTRY CONTAINS FRIEDEL PAIRS IN F_PLUS/MINUS COLUMNS
REMARK 280
REMARK 280 CRYSTAL
REMARK 280 SOLVENT CONTENT, VS (%): 54.10
REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.68
REMARK 280
REMARK 280 CRYSTALLIZATION CONDITIONS: 0.1M HEPES, 0.3M MAGNESIUM SULFATE,
REMARK 280 36% ISOPROPANOL (V/V), PH 7.5, VAPOR DIFFUSION, HANGING DROP,
REMARK 280 TEMPERATURE 277.0K
REMARK 290
REMARK 290 CRYSTALLOGRAPHIC SYMMETRY
REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 2 2 21
REMARK 290
REMARK 290 SYMOP SYMMETRY
REMARK 290 NNNMMM OPERATOR
REMARK 290 1555 X,Y,Z
REMARK 290 2555 -X,-Y,Z+1/2
REMARK 290 3555 -X,Y,-Z+1/2
REMARK 290 4555 X,-Y,-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 0.00000
REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 49.37750
REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000
REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 0.00000
REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 49.37750
REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 0.00000
REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 0.00000
REMARK 290 SMTRY3 4 0.000000 0.000000 -1.000000 0.00000
REMARK 290
REMARK 290 REMARK: NULL
REMARK 300
REMARK 300 BIOMOLECULE: 1, 2
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 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 350
REMARK 350 BIOMOLECULE: 2
REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC
REMARK 350 SOFTWARE USED: PISA
REMARK 350 TOTAL BURIED SURFACE AREA: 1810 ANGSTROM**2
REMARK 350 SURFACE AREA OF THE COMPLEX: 8510 ANGSTROM**2
REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -29.0 KCAL/MOL
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 350 BIOMT1 2 1.000000 0.000000 0.000000 0.00000
REMARK 350 BIOMT2 2 0.000000 -1.000000 0.000000 0.00000
REMARK 350 BIOMT3 2 0.000000 0.000000 -1.000000 98.75500
REMARK 620
REMARK 620 METAL COORDINATION
REMARK 620 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER;
REMARK 620 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE):
REMARK 620
REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL
REMARK 620 MG A 401 MG
REMARK 620 N RES CSSEQI ATOM
REMARK 620 1 HOH A 576 O
REMARK 620 2 HOH A 574 O 92.1
REMARK 620 3 HOH A 573 O 95.0 91.5
REMARK 620 4 HOH A 575 O 89.7 89.2 175.2
REMARK 620 5 HOH A 577 O 89.7 171.1 97.1 82.1
REMARK 620 6 HOH A 572 O 174.9 87.6 90.1 85.2 89.7
REMARK 620 N 1 2 3 4 5
REMARK 800
REMARK 800 SITE
REMARK 800 SITE_IDENTIFIER: AC1
REMARK 800 EVIDENCE_CODE: SOFTWARE
REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MG A 401
DBREF 4F2L A 284 336 UNP P54645 AAPK1_RAT 295 347
SEQADV 4F2L LEU A 337 UNP P54645 EXPRESSION TAG
SEQADV 4F2L GLU A 338 UNP P54645 EXPRESSION TAG
SEQADV 4F2L HIS A 339 UNP P54645 EXPRESSION TAG
SEQADV 4F2L HIS A 340 UNP P54645 EXPRESSION TAG
SEQADV 4F2L HIS A 341 UNP P54645 EXPRESSION TAG
SEQADV 4F2L HIS A 342 UNP P54645 EXPRESSION TAG
SEQADV 4F2L HIS A 343 UNP P54645 EXPRESSION TAG
SEQADV 4F2L HIS A 344 UNP P54645 EXPRESSION TAG
SEQRES 1 A 61 SER SER THR MSE ILE ASP ASP GLU ALA LEU LYS GLU VAL
SEQRES 2 A 61 CYS GLU LYS PHE GLU CYS SER GLU GLU GLU VAL LEU SER
SEQRES 3 A 61 CYS LEU TYR ASN ARG ASN HIS GLN ASP PRO LEU ALA VAL
SEQRES 4 A 61 ALA TYR HIS LEU ILE ILE ASP ASN ARG ARG ILE MSE ASN
SEQRES 5 A 61 GLU LEU GLU HIS HIS HIS HIS HIS HIS
MODRES 4F2L MSE A 287 MET SELENOMETHIONINE
MODRES 4F2L MSE A 334 MET SELENOMETHIONINE
HET MSE A 287 8
HET MSE A 334 8
HET MG A 401 1
HETNAM MSE SELENOMETHIONINE
HETNAM MG MAGNESIUM ION
FORMUL 1 MSE 2(C5 H11 N O2 SE)
FORMUL 2 MG MG 2+
FORMUL 3 HOH *79(H2 O)
HELIX 1 1 ASP A 289 GLU A 301 1 13
HELIX 2 2 SER A 303 ASN A 313 1 11
HELIX 3 3 ASP A 318 HIS A 344 1 27
LINK C THR A 286 N MSE A 287 1555 1555 1.33
LINK C MSE A 287 N ILE A 288 1555 1555 1.33
LINK C ILE A 333 N MSE A 334 1555 1555 1.33
LINK C MSE A 334 N ASN A 335 1555 1555 1.33
LINK MG MG A 401 O HOH A 576 1555 1555 2.01
LINK MG MG A 401 O HOH A 574 1555 1555 2.04
LINK MG MG A 401 O HOH A 573 1555 1555 2.08
LINK MG MG A 401 O HOH A 575 1555 1555 2.09
LINK MG MG A 401 O HOH A 577 1555 1555 2.30
LINK MG MG A 401 O HOH A 572 1555 1555 2.36
SITE 1 AC1 6 HOH A 572 HOH A 573 HOH A 574 HOH A 575
SITE 2 AC1 6 HOH A 576 HOH A 577
CRYST1 22.117 36.258 98.755 90.00 90.00 90.00 P 2 2 21 4
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 0.045214 0.000000 0.000000 0.00000
SCALE2 0.000000 0.027580 0.000000 0.00000
SCALE3 0.000000 0.000000 0.010126 0.00000
(ATOM LINES ARE NOT SHOWN.)
END
