HEADER DE NOVO PROTEIN 19-JAN-23 8FVT TITLE MULTI-STATE DESIGN OF TWO-STATE SWITCHABLE HINGE PROTEINS COMPND MOL_ID: 1; COMPND 2 MOLECULE: 3HB12; COMPND 3 CHAIN: A, B; COMPND 4 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: SYNTHETIC CONSTRUCT; SOURCE 3 ORGANISM_TAXID: 32630; SOURCE 4 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 5 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS DE NOVO PROTEIN, METAMORPHIC PROTEINS, SWITCHABLE HINGE PROTEINS, KEYWDS 2 PROTEIN DYNAMICS, THREE-HELIX BUNDLES EXPDTA X-RAY DIFFRACTION AUTHOR A.K.BERA,A.BROERMAN,D.BAKER REVDAT 3 06-MAR-24 8FVT 1 JRNL REVDAT 2 11-OCT-23 8FVT 1 REMARK REVDAT 1 16-AUG-23 8FVT 0 JRNL AUTH F.PRAETORIUS,P.J.Y.LEUNG,M.H.TESSMER,A.BROERMAN,C.DEMAKIS, JRNL AUTH 2 A.F.DISHMAN,A.PILLAI,A.IDRIS,D.JUERGENS,J.DAUPARAS,X.LI, JRNL AUTH 3 P.M.LEVINE,M.LAMB,R.K.BALLARD,S.R.GERBEN,H.NGUYEN,A.KANG, JRNL AUTH 4 B.SANKARAN,A.K.BERA,B.F.VOLKMAN,J.NIVALA,S.STOLL,D.BAKER JRNL TITL DESIGN OF STIMULUS-RESPONSIVE TWO-STATE HINGE PROTEINS. JRNL REF SCIENCE V. 381 754 2023 JRNL REFN ESSN 1095-9203 JRNL PMID 37590357 JRNL DOI 10.1126/SCIENCE.ADG7731 REMARK 2 REMARK 2 RESOLUTION. 3.07 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX DEV_4761 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 : GEOSTD + MONOMER LIBRARY + CDL V1.2 REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 3.07 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 47.86 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.340 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.7 REMARK 3 NUMBER OF REFLECTIONS : 3505 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.229 REMARK 3 R VALUE (WORKING SET) : 0.224 REMARK 3 FREE R VALUE : 0.274 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 9.730 REMARK 3 FREE R VALUE TEST SET COUNT : 341 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 47.8600 - 3.8700 1.00 1621 156 0.1994 0.2564 REMARK 3 2 3.8600 - 3.0700 1.00 1543 185 0.2988 0.3166 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : FLAT BULK SOLVENT MODEL REMARK 3 SOLVENT RADIUS : 1.10 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) : 0.304 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 36.728 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 95.25 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 85.94 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 : 0.004 1518 REMARK 3 ANGLE : 0.576 2026 REMARK 3 CHIRALITY : 0.027 226 REMARK 3 PLANARITY : 0.006 282 REMARK 3 DIHEDRAL : 3.933 222 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 8FVT COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 29-JAN-23. REMARK 100 THE DEPOSITION ID IS D_1000271545. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 04-NOV-22 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 7 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : ALS REMARK 200 BEAMLINE : 8.2.2 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.99998 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS PILATUS 6M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : XSCALE REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 3505 REMARK 200 RESOLUTION RANGE HIGH (A) : 3.070 REMARK 200 RESOLUTION RANGE LOW (A) : 47.860 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.6 REMARK 200 DATA REDUNDANCY : 8.800 REMARK 200 R MERGE (I) : 0.09800 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 17.3900 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 3.07 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 3.28 REMARK 200 COMPLETENESS FOR SHELL (%) : 99.5 REMARK 200 DATA REDUNDANCY IN SHELL : 9.10 REMARK 200 R MERGE FOR SHELL (I) : 0.41500 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 5.590 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: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 41.62 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.19 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 1.8 M AMMONIUM CITRATE TRIBASIC PH REMARK 280 7.0, VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 293K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: I 4 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 -Y,X,Z REMARK 290 4555 Y,-X,Z REMARK 290 5555 X+1/2,Y+1/2,Z+1/2 REMARK 290 6555 -X+1/2,-Y+1/2,Z+1/2 REMARK 290 7555 -Y+1/2,X+1/2,Z+1/2 REMARK 290 8555 Y+1/2,-X+1/2,Z+1/2 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 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 4 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY2 4 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 5 1.000000 0.000000 0.000000 33.83900 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 33.83900 REMARK 290 SMTRY3 5 0.000000 0.000000 1.000000 41.18700 REMARK 290 SMTRY1 6 -1.000000 0.000000 0.000000 33.83900 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 33.83900 REMARK 290 SMTRY3 6 0.000000 0.000000 1.000000 41.18700 REMARK 290 SMTRY1 7 0.000000 -1.000000 0.000000 33.83900 REMARK 290 SMTRY2 7 1.000000 0.000000 0.000000 33.83900 REMARK 290 SMTRY3 7 0.000000 0.000000 1.000000 41.18700 REMARK 290 SMTRY1 8 0.000000 1.000000 0.000000 33.83900 REMARK 290 SMTRY2 8 -1.000000 0.000000 0.000000 33.83900 REMARK 290 SMTRY3 8 0.000000 0.000000 1.000000 41.18700 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: DIMERIC REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, B 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 GLY A 1 REMARK 465 ALA A 98 REMARK 465 SER A 99 REMARK 465 GLU A 100 REMARK 465 GLY B 1 REMARK 465 ALA B 98 REMARK 465 SER B 99 REMARK 465 GLU B 100 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 ALA A 36 39.10 -86.72 REMARK 500 SER A 37 97.00 -63.60 REMARK 500 SER A 69 -106.65 57.15 REMARK 500 THR B 33 -156.65 -88.41 REMARK 500 REMARK 500 REMARK: NULL DBREF 8FVT A 1 100 PDB 8FVT 8FVT 1 100 DBREF 8FVT B 1 100 PDB 8FVT 8FVT 1 100 SEQRES 1 A 100 GLY LEU GLU GLU GLU ALA ARG GLU LEU ALA GLU GLU ALA SEQRES 2 A 100 ARG GLU VAL ARG ARG ARG ALA GLU GLU LEU ARG ARG ARG SEQRES 3 A 100 ALA GLU GLU ALA ARG GLU THR GLY GLU ALA SER GLU GLU SEQRES 4 A 100 HIS ALA ALA ALA LEU LEU ALA GLU ALA ALA VAL LEU GLU SEQRES 5 A 100 LEU LYS ALA VAL LEU LEU GLU LEU GLU ALA ARG ARG LEU SEQRES 6 A 100 LEU LYS GLU SER GLY GLY GLU VAL ALA ARG GLU ALA LEU SEQRES 7 A 100 GLU LEU ALA ARG GLU ALA ARG ARG GLU ALA ARG GLU ALA SEQRES 8 A 100 LEU GLU ALA ALA GLU GLU ALA SER GLU SEQRES 1 B 100 GLY LEU GLU GLU GLU ALA ARG GLU LEU ALA GLU GLU ALA SEQRES 2 B 100 ARG GLU VAL ARG ARG ARG ALA GLU GLU LEU ARG ARG ARG SEQRES 3 B 100 ALA GLU GLU ALA ARG GLU THR GLY GLU ALA SER GLU GLU SEQRES 4 B 100 HIS ALA ALA ALA LEU LEU ALA GLU ALA ALA VAL LEU GLU SEQRES 5 B 100 LEU LYS ALA VAL LEU LEU GLU LEU GLU ALA ARG ARG LEU SEQRES 6 B 100 LEU LYS GLU SER GLY GLY GLU VAL ALA ARG GLU ALA LEU SEQRES 7 B 100 GLU LEU ALA ARG GLU ALA ARG ARG GLU ALA ARG GLU ALA SEQRES 8 B 100 LEU GLU ALA ALA GLU GLU ALA SER GLU HELIX 1 AA1 LEU A 2 GLY A 34 1 33 HELIX 2 AA2 SER A 37 GLU A 68 1 32 HELIX 3 AA3 GLY A 71 GLU A 97 1 27 HELIX 4 AA4 GLU B 3 THR B 33 1 31 HELIX 5 AA5 SER B 37 SER B 69 1 33 HELIX 6 AA6 GLY B 71 GLU B 97 1 27 CRYST1 67.678 67.678 82.374 90.00 90.00 90.00 I 4 16 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 0.014776 0.000000 0.000000 0.00000 SCALE2 0.000000 0.014776 0.000000 0.00000 SCALE3 0.000000 0.000000 0.012140 0.00000