HEADER PROTEIN BINDING 24-NOV-14 4X1L
TITLE STRUCTURAL BASIS FOR MUTATION-INDUCED DESTABILIZATION OF PROFILIN 1 IN
TITLE 2 ALS
COMPND MOL_ID: 1;
COMPND 2 MOLECULE: PROFILIN-1;
COMPND 3 CHAIN: A;
COMPND 4 SYNONYM: EPIDIDYMIS TISSUE PROTEIN LI 184A,PROFILIN I;
COMPND 5 ENGINEERED: YES
SOURCE MOL_ID: 1;
SOURCE 2 ORGANISM_SCIENTIFIC: HOMO SAPIENS;
SOURCE 3 ORGANISM_COMMON: HUMAN;
SOURCE 4 ORGANISM_TAXID: 9606;
SOURCE 5 GENE: PFN1;
SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI;
SOURCE 7 EXPRESSION_SYSTEM_TAXID: 469008;
SOURCE 8 EXPRESSION_SYSTEM_STRAIN: BL21(DE3);
SOURCE 9 EXPRESSION_SYSTEM_VARIANT: PLYSS;
SOURCE 10 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID;
SOURCE 11 EXPRESSION_SYSTEM_PLASMID: PET
KEYWDS ALS, PROTEIN BINDING
EXPDTA X-RAY DIFFRACTION
AUTHOR T.V.SILVAS,S.M.D.SHANDILYA,C.A.SCHIFFER
REVDAT 7 27-SEP-23 4X1L 1 REMARK
REVDAT 6 18-DEC-19 4X1L 1 REMARK
REVDAT 5 22-NOV-17 4X1L 1 REMARK
REVDAT 4 13-SEP-17 4X1L 1 SOURCE KEYWDS JRNL REMARK
REVDAT 3 15-JUL-15 4X1L 1 JRNL
REVDAT 2 01-JUL-15 4X1L 1 JRNL
REVDAT 1 10-JUN-15 4X1L 0
JRNL AUTH S.BOOPATHY,T.V.SILVAS,M.TISCHBEIN,S.JANSEN,S.M.SHANDILYA,
JRNL AUTH 2 J.A.ZITZEWITZ,J.E.LANDERS,B.L.GOODE,C.A.SCHIFFER,D.A.BOSCO
JRNL TITL STRUCTURAL BASIS FOR MUTATION-INDUCED DESTABILIZATION OF
JRNL TITL 2 PROFILIN 1 IN ALS.
JRNL REF PROC.NATL.ACAD.SCI.USA V. 112 7984 2015
JRNL REFN ESSN 1091-6490
JRNL PMID 26056300
JRNL DOI 10.1073/PNAS.1424108112
REMARK 2
REMARK 2 RESOLUTION. 2.16 ANGSTROMS.
REMARK 3
REMARK 3 REFINEMENT.
REMARK 3 PROGRAM : PHENIX (PHENIX.REFINE: 1.9_1692)
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) : 2.16
REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 27.90
REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.340
REMARK 3 COMPLETENESS FOR RANGE (%) : 99.3
REMARK 3 NUMBER OF REFLECTIONS : 6579
REMARK 3
REMARK 3 FIT TO DATA USED IN REFINEMENT.
REMARK 3 R VALUE (WORKING + TEST SET) : 0.217
REMARK 3 R VALUE (WORKING SET) : 0.216
REMARK 3 FREE R VALUE : 0.247
REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.680
REMARK 3 FREE R VALUE TEST SET COUNT : 308
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 27.8975 - 2.7211 0.99 3167 162 0.2001 0.2338
REMARK 3 2 2.7211 - 2.1601 0.99 3104 146 0.2592 0.2837
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) : 0.300
REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 27.800
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) : 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 : 0.002 924
REMARK 3 ANGLE : 0.616 1256
REMARK 3 CHIRALITY : 0.023 150
REMARK 3 PLANARITY : 0.002 158
REMARK 3 DIHEDRAL : 10.829 309
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 4X1L COMPLIES WITH FORMAT V. 3.30, 13-JUL-11
REMARK 100
REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 25-NOV-14.
REMARK 100 THE DEPOSITION ID IS D_1000204778.
REMARK 200
REMARK 200 EXPERIMENTAL DETAILS
REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION
REMARK 200 DATE OF DATA COLLECTION : 05-JUN-13
REMARK 200 TEMPERATURE (KELVIN) : 100
REMARK 200 PH : 6.0
REMARK 200 NUMBER OF CRYSTALS USED : NULL
REMARK 200
REMARK 200 SYNCHROTRON (Y/N) : N
REMARK 200 RADIATION SOURCE : ROTATING ANODE
REMARK 200 BEAMLINE : NULL
REMARK 200 X-RAY GENERATOR MODEL : RIGAKU MICROMAX-007 HF
REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M
REMARK 200 WAVELENGTH OR RANGE (A) : 1.5418
REMARK 200 MONOCHROMATOR : NULL
REMARK 200 OPTICS : OSMIC MIRRORS
REMARK 200
REMARK 200 DETECTOR TYPE : CCD
REMARK 200 DETECTOR MANUFACTURER : RIGAKU SATURN 944+
REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS
REMARK 200 DATA SCALING SOFTWARE : XIA2, SCALA
REMARK 200
REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 6584
REMARK 200 RESOLUTION RANGE HIGH (A) : 2.160
REMARK 200 RESOLUTION RANGE LOW (A) : 27.900
REMARK 200 REJECTION CRITERIA (SIGMA(I)) : -2.000
REMARK 200
REMARK 200 OVERALL.
REMARK 200 COMPLETENESS FOR RANGE (%) : 99.3
REMARK 200 DATA REDUNDANCY : 3.200
REMARK 200 R MERGE (I) : 0.07500
REMARK 200 R SYM (I) : NULL
REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 13.3000
REMARK 200
REMARK 200 IN THE HIGHEST RESOLUTION SHELL.
REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.16
REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.24
REMARK 200 COMPLETENESS FOR SHELL (%) : 98.9
REMARK 200 DATA REDUNDANCY IN SHELL : 3.20
REMARK 200 R MERGE FOR SHELL (I) : 0.58900
REMARK 200 R SYM FOR SHELL (I) : NULL
REMARK 200 <I/SIGMA(I)> FOR SHELL : 2.300
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: 1FIK
REMARK 200
REMARK 200 REMARK: NULL
REMARK 280
REMARK 280 CRYSTAL
REMARK 280 SOLVENT CONTENT, VS (%): 39.32
REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.03
REMARK 280
REMARK 280 CRYSTALLIZATION CONDITIONS: PFN1 CRYSTALS WERE GROWN BY HANGING
REMARK 280 DROP VAPOR DIFFUSION AFTER MIXING THE PFN1 PROTEIN WITH A 1:1
REMARK 280 RATIO OF RESERVOIR SOLUTION AT 298K FOR WT. RESERVOIR SOLUTION
REMARK 280 FOR WT CONTAINED 50 MM KH2PO4, 36% (WT/VOL) PEG 8,000 AND 100 MM
REMARK 280 MES PH 6.0., VAPOR DIFFUSION, HANGING DROP
REMARK 290
REMARK 290 CRYSTALLOGRAPHIC SYMMETRY
REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: C 1 2 1
REMARK 290
REMARK 290 SYMOP SYMMETRY
REMARK 290 NNNMMM OPERATOR
REMARK 290 1555 X,Y,Z
REMARK 290 2555 -X,Y,-Z
REMARK 290 3555 X+1/2,Y+1/2,Z
REMARK 290 4555 -X+1/2,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 0.00000
REMARK 290 SMTRY3 2 0.000000 0.000000 -1.000000 0.00000
REMARK 290 SMTRY1 3 1.000000 0.000000 0.000000 37.13000
REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 15.92000
REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 0.00000
REMARK 290 SMTRY1 4 -1.000000 0.000000 0.000000 37.13000
REMARK 290 SMTRY2 4 0.000000 1.000000 0.000000 15.92000
REMARK 290 SMTRY3 4 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 MET A 1
REMARK 465 ALA A 2
REMARK 465 SER A 57
REMARK 465 SER A 58
REMARK 465 PHE A 59
REMARK 465 TYR A 60
REMARK 465 VAL A 61
REMARK 465 ASN A 62
REMARK 465 SER A 92
REMARK 465 THR A 93
REMARK 465 GLY A 94
REMARK 465 GLY A 95
REMARK 465 ALA A 96
REMARK 470
REMARK 470 MISSING ATOM
REMARK 470 THE FOLLOWING RESIDUES HAVE MISSING ATOMS (M=MODEL NUMBER;
REMARK 470 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER;
REMARK 470 I=INSERTION CODE):
REMARK 470 M RES CSSEQI ATOMS
REMARK 470 LYS A 54 CG CD CE NZ
REMARK 470 LYS A 70 CG CD CE NZ
REMARK 470 ILE A 74 CG1 CG2 CD1
REMARK 470 ARG A 75 CG CD NE CZ NH1 NH2
REMARK 470 LEU A 79 CG CD1 CD2
REMARK 470 GLN A 80 CG CD OE1 NE2
REMARK 470 ASP A 81 CG OD1 OD2
REMARK 470 GLU A 83 CG CD OE1 OE2
REMARK 470 ARG A 89 CG CD NE CZ NH1 NH2
REMARK 470 LYS A 91 CG CD CE NZ
REMARK 470 LYS A 108 CG CD CE NZ
REMARK 470 GLU A 117 CG CD OE1 OE2
REMARK 470 ARG A 137 CG CD NE CZ NH1 NH2
REMARK 470 GLN A 139 CG CD OE1 NE2
REMARK 500
REMARK 500 GEOMETRY AND STEREOCHEMISTRY
REMARK 500 SUBTOPIC: CLOSE CONTACTS IN SAME ASYMMETRIC UNIT
REMARK 500
REMARK 500 THE FOLLOWING ATOMS ARE IN CLOSE CONTACT.
REMARK 500
REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI DISTANCE
REMARK 500 O HOH A 327 O HOH A 352 1.87
REMARK 500 O HOH A 355 O HOH A 360 2.05
REMARK 500 O HOH A 323 O HOH A 358 2.13
REMARK 500 O HOH A 360 O HOH A 361 2.15
REMARK 500
REMARK 500 REMARK: NULL
REMARK 500
REMARK 500 GEOMETRY AND STEREOCHEMISTRY
REMARK 500 SUBTOPIC: TORSION ANGLES
REMARK 500
REMARK 500 TORSION ANGLES OUTSIDE THE EXPECTED RAMACHANDRAN REGIONS:
REMARK 500 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER;
REMARK 500 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE).
REMARK 500
REMARK 500 STANDARD TABLE:
REMARK 500 FORMAT:(10X,I3,1X,A3,1X,A1,I4,A1,4X,F7.2,3X,F7.2)
REMARK 500
REMARK 500 EXPECTED VALUES: GJ KLEYWEGT AND TA JONES (1996). PHI/PSI-
REMARK 500 CHOLOGY: RAMACHANDRAN REVISITED. STRUCTURE 4, 1395 - 1400
REMARK 500
REMARK 500 M RES CSSEQI PSI PHI
REMARK 500 ASP A 27 -69.73 59.82
REMARK 500 LYS A 38 -146.93 -117.32
REMARK 500 LYS A 108 -4.17 -143.18
REMARK 500
REMARK 500 REMARK: NULL
REMARK 800
REMARK 800 SITE
REMARK 800 SITE_IDENTIFIER: AC1
REMARK 800 EVIDENCE_CODE: SOFTWARE
REMARK 800 SITE_DESCRIPTION: binding site for residue PO4 A 201
REMARK 900
REMARK 900 RELATED ENTRIES
REMARK 900 RELATED ID: 4X1M RELATED DB: PDB
REMARK 900 RELATED ID: 4X25 RELATED DB: PDB
DBREF 4X1L A 1 140 UNP P07737 PROF1_HUMAN 1 140
SEQRES 1 A 140 MET ALA GLY TRP ASN ALA TYR ILE ASP ASN LEU MET ALA
SEQRES 2 A 140 ASP GLY THR CYS GLN ASP ALA ALA ILE VAL GLY TYR LYS
SEQRES 3 A 140 ASP SER PRO SER VAL TRP ALA ALA VAL PRO GLY LYS THR
SEQRES 4 A 140 PHE VAL ASN ILE THR PRO ALA GLU VAL GLY VAL LEU VAL
SEQRES 5 A 140 GLY LYS ASP ARG SER SER PHE TYR VAL ASN GLY LEU THR
SEQRES 6 A 140 LEU GLY GLY GLN LYS CYS SER VAL ILE ARG ASP SER LEU
SEQRES 7 A 140 LEU GLN ASP GLY GLU PHE SER MET ASP LEU ARG THR LYS
SEQRES 8 A 140 SER THR GLY GLY ALA PRO THR PHE ASN VAL THR VAL THR
SEQRES 9 A 140 LYS THR ASP LYS THR LEU VAL LEU LEU MET GLY LYS GLU
SEQRES 10 A 140 GLY VAL HIS GLY GLY LEU ILE ASN LYS LYS CYS TYR GLU
SEQRES 11 A 140 MET ALA SER HIS LEU ARG ARG SER GLN TYR
HET PO4 A 201 5
HETNAM PO4 PHOSPHATE ION
FORMUL 2 PO4 O4 P 3-
FORMUL 3 HOH *64(H2 O)
HELIX 1 AA1 TRP A 4 MET A 12 1 9
HELIX 2 AA2 THR A 39 ILE A 43 5 5
HELIX 3 AA3 THR A 44 VAL A 52 1 9
HELIX 4 AA4 HIS A 120 ARG A 137 1 18
SHEET 1 AA1 7 SER A 30 ALA A 34 0
SHEET 2 AA1 7 CYS A 17 GLY A 24 -1 N ILE A 22 O ALA A 33
SHEET 3 AA1 7 THR A 109 GLY A 115 -1 O MET A 114 N ASP A 19
SHEET 4 AA1 7 ASN A 100 LYS A 105 -1 N THR A 104 O VAL A 111
SHEET 5 AA1 7 SER A 85 THR A 90 -1 N LEU A 88 O VAL A 101
SHEET 6 AA1 7 GLN A 69 SER A 77 -1 N SER A 72 O ARG A 89
SHEET 7 AA1 7 LEU A 64 LEU A 66 -1 N LEU A 64 O CYS A 71
SITE 1 AC1 3 ASN A 100 HIS A 120 GLY A 121
CRYST1 74.260 31.840 61.020 90.00 122.66 90.00 C 1 2 1 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 0.013466 0.000000 0.008632 0.00000
SCALE2 0.000000 0.031407 0.000000 0.00000
SCALE3 0.000000 0.000000 0.019466 0.00000
(ATOM LINES ARE NOT SHOWN.)
END
