HEADER APOPTOSIS 23-OCT-15 5EFM
TITLE BECLIN 1 FLEXIBLE-HELICAL DOMIAN (FHD) (141-171)
COMPND MOL_ID: 1;
COMPND 2 MOLECULE: BECLIN-1;
COMPND 3 CHAIN: A;
COMPND 4 SYNONYM: COILED-COIL MYOSIN-LIKE BCL2-INTERACTING PROTEIN,PROTEIN
COMPND 5 GT197;
COMPND 6 ENGINEERED: YES
SOURCE MOL_ID: 1;
SOURCE 2 SYNTHETIC: YES;
SOURCE 3 ORGANISM_SCIENTIFIC: HOMO SAPIENS;
SOURCE 4 ORGANISM_COMMON: HUMAN;
SOURCE 5 ORGANISM_TAXID: 9606
KEYWDS FLEXIBLE HELIX, APOPTOSIS
EXPDTA X-RAY DIFFRACTION
AUTHOR S.SINHA,Y.MEI
REVDAT 3 16-OCT-24 5EFM 1 REMARK
REVDAT 2 22-NOV-17 5EFM 1 JRNL REMARK
REVDAT 1 20-JUL-16 5EFM 0
JRNL AUTH Y.MEI,A.RAMANATHAN,K.GLOVER,C.STANLEY,R.SANISHVILI,
JRNL AUTH 2 S.CHAKRAVARTHY,Z.YANG,C.L.COLBERT,S.C.SINHA
JRNL TITL CONFORMATIONAL FLEXIBILITY ENABLES THE FUNCTION OF A BECN1
JRNL TITL 2 REGION ESSENTIAL FOR STARVATION-MEDIATED AUTOPHAGY.
JRNL REF BIOCHEMISTRY V. 55 1945 2016
JRNL REFN ISSN 0006-2960
JRNL PMID 26937551
JRNL DOI 10.1021/ACS.BIOCHEM.5B01264
REMARK 2
REMARK 2 RESOLUTION. 1.95 ANGSTROMS.
REMARK 3
REMARK 3 REFINEMENT.
REMARK 3 PROGRAM : PHENIX
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) : 1.95
REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 44.66
REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.340
REMARK 3 COMPLETENESS FOR RANGE (%) : 100.0
REMARK 3 NUMBER OF REFLECTIONS : 3490
REMARK 3
REMARK 3 FIT TO DATA USED IN REFINEMENT.
REMARK 3 R VALUE (WORKING + TEST SET) : 0.212
REMARK 3 R VALUE (WORKING SET) : 0.212
REMARK 3 FREE R VALUE : 0.216
REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.840
REMARK 3 FREE R VALUE TEST SET COUNT : 169
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 0.0000 - 1.9500 1.00 3321 169 0.2116 0.2164
REMARK 3
REMARK 3 BULK SOLVENT MODELLING.
REMARK 3 METHOD USED : FLAT BULK SOLVENT MODEL
REMARK 3 SOLVENT RADIUS : 1.11
REMARK 3 SHRINKAGE RADIUS : 0.90
REMARK 3 K_SOL : NULL
REMARK 3 B_SOL : NULL
REMARK 3
REMARK 3 ERROR ESTIMATES.
REMARK 3 COORDINATE ERROR (MAXIMUM-LIKELIHOOD BASED) : 0.040
REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 32.450
REMARK 3
REMARK 3 B VALUES.
REMARK 3 FROM WILSON PLOT (A**2) : NULL
REMARK 3 MEAN B VALUE (OVERALL, A**2) : 54.53
REMARK 3 OVERALL ANISOTROPIC B VALUE.
REMARK 3 B11 (A**2) : NULL
REMARK 3 B22 (A**2) : NULL
REMARK 3 B33 (A**2) : NULL
REMARK 3 B12 (A**2) : NULL
REMARK 3 B13 (A**2) : NULL
REMARK 3 B23 (A**2) : NULL
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 : 0.009 147
REMARK 3 ANGLE : 1.298 196
REMARK 3 CHIRALITY : 0.068 19
REMARK 3 PLANARITY : 0.004 27
REMARK 3 DIHEDRAL : 13.696 61
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: NULL
REMARK 4
REMARK 4 5EFM COMPLIES WITH FORMAT V. 3.30, 13-JUL-11
REMARK 100
REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 26-OCT-15.
REMARK 100 THE DEPOSITION ID IS D_1000214787.
REMARK 200
REMARK 200 EXPERIMENTAL DETAILS
REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION
REMARK 200 DATE OF DATA COLLECTION : 26-JUN-12
REMARK 200 TEMPERATURE (KELVIN) : 100
REMARK 200 PH : 5.6
REMARK 200 NUMBER OF CRYSTALS USED : 1
REMARK 200
REMARK 200 SYNCHROTRON (Y/N) : Y
REMARK 200 RADIATION SOURCE : APS
REMARK 200 BEAMLINE : 23-ID-D
REMARK 200 X-RAY GENERATOR MODEL : NULL
REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M
REMARK 200 WAVELENGTH OR RANGE (A) : 1.3776
REMARK 200 MONOCHROMATOR : SI (111)
REMARK 200 OPTICS : NULL
REMARK 200
REMARK 200 DETECTOR TYPE : IMAGE PLATE
REMARK 200 DETECTOR MANUFACTURER : MAR SCANNER 300 MM PLATE
REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS
REMARK 200 DATA SCALING SOFTWARE : XDS, XSCALE
REMARK 200
REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 3490
REMARK 200 RESOLUTION RANGE HIGH (A) : 1.950
REMARK 200 RESOLUTION RANGE LOW (A) : 44.660
REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL
REMARK 200
REMARK 200 OVERALL.
REMARK 200 COMPLETENESS FOR RANGE (%) : 100.0
REMARK 200 DATA REDUNDANCY : 75.50
REMARK 200 R MERGE (I) : NULL
REMARK 200 R SYM (I) : 0.16000
REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 26.3000
REMARK 200
REMARK 200 IN THE HIGHEST RESOLUTION SHELL.
REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.95
REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.05
REMARK 200 COMPLETENESS FOR SHELL (%) : 100.0
REMARK 200 DATA REDUNDANCY IN SHELL : 78.10
REMARK 200 R MERGE FOR SHELL (I) : NULL
REMARK 200 R SYM FOR SHELL (I) : NULL
REMARK 200 <I/SIGMA(I)> FOR SHELL : 1.800
REMARK 200
REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH
REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: SAD
REMARK 200 SOFTWARE USED: SHELXD
REMARK 200 STARTING MODEL: NULL
REMARK 200
REMARK 200 REMARK: NULL
REMARK 280
REMARK 280 CRYSTAL
REMARK 280 SOLVENT CONTENT, VS (%): 56.82
REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.85
REMARK 280
REMARK 280 CRYSTALLIZATION CONDITIONS: 250MM POTASSIUM SODIUM TARTRATE
REMARK 280 TETRAHYDRATE, 2.2 M AMMONIUM SULFATE, 100MM SODIUM CITRATE
REMARK 280 TRIBASIC DIHYDRATE (PH 5.6), EVAPORATION, TEMPERATURE 293K
REMARK 290
REMARK 290 CRYSTALLOGRAPHIC SYMMETRY
REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 43 3 2
REMARK 290
REMARK 290 SYMOP SYMMETRY
REMARK 290 NNNMMM OPERATOR
REMARK 290 1555 X,Y,Z
REMARK 290 2555 -X+1/2,-Y,Z+1/2
REMARK 290 3555 -X,Y+1/2,-Z+1/2
REMARK 290 4555 X+1/2,-Y+1/2,-Z
REMARK 290 5555 Z,X,Y
REMARK 290 6555 Z+1/2,-X+1/2,-Y
REMARK 290 7555 -Z+1/2,-X,Y+1/2
REMARK 290 8555 -Z,X+1/2,-Y+1/2
REMARK 290 9555 Y,Z,X
REMARK 290 10555 -Y,Z+1/2,-X+1/2
REMARK 290 11555 Y+1/2,-Z+1/2,-X
REMARK 290 12555 -Y+1/2,-Z,X+1/2
REMARK 290 13555 Y+1/4,X+3/4,-Z+3/4
REMARK 290 14555 -Y+1/4,-X+1/4,-Z+1/4
REMARK 290 15555 Y+3/4,-X+3/4,Z+1/4
REMARK 290 16555 -Y+3/4,X+1/4,Z+3/4
REMARK 290 17555 X+1/4,Z+3/4,-Y+3/4
REMARK 290 18555 -X+3/4,Z+1/4,Y+3/4
REMARK 290 19555 -X+1/4,-Z+1/4,-Y+1/4
REMARK 290 20555 X+3/4,-Z+3/4,Y+1/4
REMARK 290 21555 Z+1/4,Y+3/4,-X+3/4
REMARK 290 22555 Z+3/4,-Y+3/4,X+1/4
REMARK 290 23555 -Z+3/4,Y+1/4,X+3/4
REMARK 290 24555 -Z+1/4,-Y+1/4,-X+1/4
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 31.58150
REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000
REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 31.58150
REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000
REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 31.58150
REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 31.58150
REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 31.58150
REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 31.58150
REMARK 290 SMTRY3 4 0.000000 0.000000 -1.000000 0.00000
REMARK 290 SMTRY1 5 0.000000 0.000000 1.000000 0.00000
REMARK 290 SMTRY2 5 1.000000 0.000000 0.000000 0.00000
REMARK 290 SMTRY3 5 0.000000 1.000000 0.000000 0.00000
REMARK 290 SMTRY1 6 0.000000 0.000000 1.000000 31.58150
REMARK 290 SMTRY2 6 -1.000000 0.000000 0.000000 31.58150
REMARK 290 SMTRY3 6 0.000000 -1.000000 0.000000 0.00000
REMARK 290 SMTRY1 7 0.000000 0.000000 -1.000000 31.58150
REMARK 290 SMTRY2 7 -1.000000 0.000000 0.000000 0.00000
REMARK 290 SMTRY3 7 0.000000 1.000000 0.000000 31.58150
REMARK 290 SMTRY1 8 0.000000 0.000000 -1.000000 0.00000
REMARK 290 SMTRY2 8 1.000000 0.000000 0.000000 31.58150
REMARK 290 SMTRY3 8 0.000000 -1.000000 0.000000 31.58150
REMARK 290 SMTRY1 9 0.000000 1.000000 0.000000 0.00000
REMARK 290 SMTRY2 9 0.000000 0.000000 1.000000 0.00000
REMARK 290 SMTRY3 9 1.000000 0.000000 0.000000 0.00000
REMARK 290 SMTRY1 10 0.000000 -1.000000 0.000000 0.00000
REMARK 290 SMTRY2 10 0.000000 0.000000 1.000000 31.58150
REMARK 290 SMTRY3 10 -1.000000 0.000000 0.000000 31.58150
REMARK 290 SMTRY1 11 0.000000 1.000000 0.000000 31.58150
REMARK 290 SMTRY2 11 0.000000 0.000000 -1.000000 31.58150
REMARK 290 SMTRY3 11 -1.000000 0.000000 0.000000 0.00000
REMARK 290 SMTRY1 12 0.000000 -1.000000 0.000000 31.58150
REMARK 290 SMTRY2 12 0.000000 0.000000 -1.000000 0.00000
REMARK 290 SMTRY3 12 1.000000 0.000000 0.000000 31.58150
REMARK 290 SMTRY1 13 0.000000 1.000000 0.000000 15.79075
REMARK 290 SMTRY2 13 1.000000 0.000000 0.000000 47.37225
REMARK 290 SMTRY3 13 0.000000 0.000000 -1.000000 47.37225
REMARK 290 SMTRY1 14 0.000000 -1.000000 0.000000 15.79075
REMARK 290 SMTRY2 14 -1.000000 0.000000 0.000000 15.79075
REMARK 290 SMTRY3 14 0.000000 0.000000 -1.000000 15.79075
REMARK 290 SMTRY1 15 0.000000 1.000000 0.000000 47.37225
REMARK 290 SMTRY2 15 -1.000000 0.000000 0.000000 47.37225
REMARK 290 SMTRY3 15 0.000000 0.000000 1.000000 15.79075
REMARK 290 SMTRY1 16 0.000000 -1.000000 0.000000 47.37225
REMARK 290 SMTRY2 16 1.000000 0.000000 0.000000 15.79075
REMARK 290 SMTRY3 16 0.000000 0.000000 1.000000 47.37225
REMARK 290 SMTRY1 17 1.000000 0.000000 0.000000 15.79075
REMARK 290 SMTRY2 17 0.000000 0.000000 1.000000 47.37225
REMARK 290 SMTRY3 17 0.000000 -1.000000 0.000000 47.37225
REMARK 290 SMTRY1 18 -1.000000 0.000000 0.000000 47.37225
REMARK 290 SMTRY2 18 0.000000 0.000000 1.000000 15.79075
REMARK 290 SMTRY3 18 0.000000 1.000000 0.000000 47.37225
REMARK 290 SMTRY1 19 -1.000000 0.000000 0.000000 15.79075
REMARK 290 SMTRY2 19 0.000000 0.000000 -1.000000 15.79075
REMARK 290 SMTRY3 19 0.000000 -1.000000 0.000000 15.79075
REMARK 290 SMTRY1 20 1.000000 0.000000 0.000000 47.37225
REMARK 290 SMTRY2 20 0.000000 0.000000 -1.000000 47.37225
REMARK 290 SMTRY3 20 0.000000 1.000000 0.000000 15.79075
REMARK 290 SMTRY1 21 0.000000 0.000000 1.000000 15.79075
REMARK 290 SMTRY2 21 0.000000 1.000000 0.000000 47.37225
REMARK 290 SMTRY3 21 -1.000000 0.000000 0.000000 47.37225
REMARK 290 SMTRY1 22 0.000000 0.000000 1.000000 47.37225
REMARK 290 SMTRY2 22 0.000000 -1.000000 0.000000 47.37225
REMARK 290 SMTRY3 22 1.000000 0.000000 0.000000 15.79075
REMARK 290 SMTRY1 23 0.000000 0.000000 -1.000000 47.37225
REMARK 290 SMTRY2 23 0.000000 1.000000 0.000000 15.79075
REMARK 290 SMTRY3 23 1.000000 0.000000 0.000000 47.37225
REMARK 290 SMTRY1 24 0.000000 0.000000 -1.000000 15.79075
REMARK 290 SMTRY2 24 0.000000 -1.000000 0.000000 15.79075
REMARK 290 SMTRY3 24 -1.000000 0.000000 0.000000 15.79075
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: TRIMERIC
REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: TRIMERIC
REMARK 350 SOFTWARE USED: PISA
REMARK 350 TOTAL BURIED SURFACE AREA: 2470 ANGSTROM**2
REMARK 350 SURFACE AREA OF THE COMPLEX: 3530 ANGSTROM**2
REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -77.0 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 0.000000 0.000000 1.000000 31.58150
REMARK 350 BIOMT2 2 -1.000000 0.000000 0.000000 94.74450
REMARK 350 BIOMT3 2 0.000000 -1.000000 0.000000 63.16300
REMARK 350 BIOMT1 3 0.000000 -1.000000 0.000000 94.74450
REMARK 350 BIOMT2 3 0.000000 0.000000 -1.000000 63.16300
REMARK 350 BIOMT3 3 1.000000 0.000000 0.000000 -31.58150
REMARK 375
REMARK 375 SPECIAL POSITION
REMARK 375 THE FOLLOWING ATOMS ARE FOUND TO BE WITHIN 0.15 ANGSTROMS
REMARK 375 OF A SYMMETRY RELATED ATOM AND ARE ASSUMED TO BE ON SPECIAL
REMARK 375 POSITIONS.
REMARK 375
REMARK 375 ATOM RES CSSEQI
REMARK 375 S SO4 A 201 LIES ON A SPECIAL POSITION.
REMARK 375 O3 SO4 A 201 LIES ON A SPECIAL POSITION.
REMARK 375 HOH A 306 LIES ON A SPECIAL POSITION.
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 THR A 141
REMARK 465 ASP A 142
REMARK 465 THR A 143
REMARK 465 LEU A 144
REMARK 465 LEU A 145
REMARK 465 ASP A 146
REMARK 465 GLN A 147
REMARK 465 LEU A 148
REMARK 465 ASP A 149
REMARK 465 THR A 150
REMARK 465 GLN A 151
REMARK 465 LEU A 152
REMARK 465 ASN A 153
REMARK 465 VAL A 154
REMARK 465 THR A 155
REMARK 465 GLU A 156
REMARK 800
REMARK 800 SITE
REMARK 800 SITE_IDENTIFIER: AC1
REMARK 800 EVIDENCE_CODE: SOFTWARE
REMARK 800 SITE_DESCRIPTION: binding site for residue SO4 A 201
DBREF 5EFM A 141 171 UNP Q14457 BECN1_HUMAN 141 171
SEQRES 1 A 31 THR ASP THR LEU LEU ASP GLN LEU ASP THR GLN LEU ASN
SEQRES 2 A 31 VAL THR GLU ASN GLU CYS GLN ASN TYR LYS ARG CYS LEU
SEQRES 3 A 31 GLU ILE LEU GLU GLN
HET SO4 A 201 5
HETNAM SO4 SULFATE ION
FORMUL 2 SO4 O4 S 2-
FORMUL 3 HOH *8(H2 O)
HELIX 1 AA1 CYS A 159 GLU A 170 1 12
SSBOND 1 CYS A 159 CYS A 165 1555 6566 2.06
SITE 1 AC1 2 ASN A 161 TYR A 162
CRYST1 63.163 63.163 63.163 90.00 90.00 90.00 P 43 3 2 24
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 0.015832 0.000000 0.000000 0.00000
SCALE2 0.000000 0.015832 0.000000 0.00000
SCALE3 0.000000 0.000000 0.015832 0.00000
(ATOM LINES ARE NOT SHOWN.)
END
