HEADER DE NOVO PROTEIN 17-OCT-18 6MSQ TITLE CRYSTAL STRUCTURE OF PRO-2.3 COMPND MOL_ID: 1; COMPND 2 MOLECULE: PRO-2.3; 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, COMPUTATIONAL DESIGN, HELICAL BUNDLE EXPDTA X-RAY DIFFRACTION AUTHOR S.E.BOYKEN,B.SANKARAN,M.J.BICK,D.BAKER REVDAT 6 03-APR-24 6MSQ 1 REMARK REVDAT 5 13-MAR-24 6MSQ 1 REMARK REVDAT 4 18-MAR-20 6MSQ 1 AUTHOR REVDAT 3 20-NOV-19 6MSQ 1 REMARK REVDAT 2 29-MAY-19 6MSQ 1 TITLE JRNL REVDAT 1 08-MAY-19 6MSQ 0 JRNL AUTH S.E.BOYKEN,M.A.BENHAIM,F.BUSCH,M.JIA,M.J.BICK,H.CHOI, JRNL AUTH 2 J.C.KLIMA,Z.CHEN,C.WALKEY,A.MILEANT,A.SAHASRABUDDHE,K.Y.WEI, JRNL AUTH 3 E.A.HODGE,S.BYRON,A.QUIJANO-RUBIO,B.SANKARAN,N.P.KING, JRNL AUTH 4 J.LIPPINCOTT-SCHWARTZ,V.H.WYSOCKI,K.K.LEE,D.BAKER JRNL TITL DE NOVO DESIGN OF TUNABLE, PH-DRIVEN CONFORMATIONAL CHANGES. JRNL REF SCIENCE V. 364 658 2019 JRNL REFN ESSN 1095-9203 JRNL PMID 31097662 JRNL DOI 10.1126/SCIENCE.AAV7897 REMARK 2 REMARK 2 RESOLUTION. 1.28 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX (DEV_3112: ???) 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 : NULL REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.28 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 43.79 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 83.6 REMARK 3 NUMBER OF REFLECTIONS : 40645 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.174 REMARK 3 R VALUE (WORKING SET) : 0.173 REMARK 3 FREE R VALUE : 0.194 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.080 REMARK 3 FREE R VALUE TEST SET COUNT : 1657 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 43.8173 - 2.9302 0.97 3837 157 0.1553 0.1676 REMARK 3 2 2.9302 - 2.3258 1.00 3886 172 0.1520 0.1617 REMARK 3 3 2.3258 - 2.0318 0.98 3795 165 0.1534 0.1845 REMARK 3 4 2.0318 - 1.8461 0.94 3668 166 0.1739 0.1978 REMARK 3 5 1.8461 - 1.7137 0.94 3653 159 0.1645 0.1930 REMARK 3 6 1.7137 - 1.6127 0.93 3599 138 0.1545 0.1818 REMARK 3 7 1.6127 - 1.5319 0.88 3430 142 0.1637 0.2114 REMARK 3 8 1.5319 - 1.4652 0.77 3018 125 0.2505 0.3463 REMARK 3 9 1.4652 - 1.4088 0.71 2710 119 0.3031 0.3114 REMARK 3 10 1.4088 - 1.3602 0.72 2797 126 0.4008 0.4592 REMARK 3 11 1.3602 - 1.3177 0.62 2412 98 0.3900 0.4191 REMARK 3 12 1.3177 - 1.2800 0.56 2183 90 0.4998 0.5024 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : NULL 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) : 0.200 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 30.240 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 : 0.007 1182 REMARK 3 ANGLE : 0.731 1605 REMARK 3 CHIRALITY : 0.044 202 REMARK 3 PLANARITY : 0.005 209 REMARK 3 DIHEDRAL : 18.755 446 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 6MSQ COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 18-OCT-18. REMARK 100 THE DEPOSITION ID IS D_1000237520. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 26-JAN-18 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 8.0 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) : 0.999913 REMARK 200 MONOCHROMATOR : DOUBLE-CRYSTAL SI(111) REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 315R REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS JUN 17, 2015 REMARK 200 DATA SCALING SOFTWARE : XDS JUN 17, 2015 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 48515 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.280 REMARK 200 RESOLUTION RANGE LOW (A) : 43.790 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.8 REMARK 200 DATA REDUNDANCY : 8.800 REMARK 200 R MERGE (I) : 0.11700 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 7.8000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.28 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.30 REMARK 200 COMPLETENESS FOR SHELL (%) : 100.0 REMARK 200 DATA REDUNDANCY IN SHELL : 6.40 REMARK 200 R MERGE FOR SHELL (I) : 3.55400 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 0.500 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: PHASER 2.7.16 REMARK 200 STARTING MODEL: COMPUTATIONAL DESIGN MODEL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 56.73 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.84 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.2M DI-SODIUM TARTRATE AND 20% W/V REMARK 280 PEG 3350, PH 8.0, VAPOR DIFFUSION, SITTING DROP, TEMPERATURE REMARK 280 290.15K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 63 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -Y,X-Y,Z REMARK 290 3555 -X+Y,-X,Z REMARK 290 4555 -X,-Y,Z+1/2 REMARK 290 5555 Y,-X+Y,Z+1/2 REMARK 290 6555 X-Y,X,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 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 2 0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 3 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 3 -0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 0.00000 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 65.37650 REMARK 290 SMTRY1 5 0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 5 -0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 5 0.000000 0.000000 1.000000 65.37650 REMARK 290 SMTRY1 6 0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 6 0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 6 0.000000 0.000000 1.000000 65.37650 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: TRIMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: TRIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 5990 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 11460 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -42.0 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 -0.500000 -0.866025 0.000000 50.56600 REMARK 350 BIOMT2 2 0.866025 -0.500000 0.000000 0.00000 REMARK 350 BIOMT3 2 0.000000 0.000000 1.000000 0.00000 REMARK 350 BIOMT1 3 -0.500000 0.866025 0.000000 25.28300 REMARK 350 BIOMT2 3 -0.866025 -0.500000 0.000000 43.79144 REMARK 350 BIOMT3 3 0.000000 0.000000 1.000000 0.00000 REMARK 350 REMARK 350 BIOMOLECULE: 2 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: 6180 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 11260 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -50.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: 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 350 BIOMT1 2 -0.500000 -0.866025 0.000000 0.00000 REMARK 350 BIOMT2 2 0.866025 -0.500000 0.000000 0.00000 REMARK 350 BIOMT3 2 0.000000 0.000000 1.000000 0.00000 REMARK 350 BIOMT1 3 -0.500000 0.866025 0.000000 0.00000 REMARK 350 BIOMT2 3 -0.866025 -0.500000 0.000000 0.00000 REMARK 350 BIOMT3 3 0.000000 0.000000 1.000000 0.00000 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 HOH A 156 LIES ON A SPECIAL POSITION. REMARK 375 HOH B 156 LIES ON A SPECIAL POSITION. 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 GLU A 2 CG CD OE1 OE2 REMARK 470 GLU A 4 OE1 OE2 REMARK 470 LYS A 7 NZ REMARK 470 LYS A 13 CE NZ REMARK 470 LYS A 20 NZ REMARK 470 GLU A 31 CD OE1 OE2 REMARK 470 LYS A 35 CE NZ REMARK 470 LYS A 75 CA C O CB CG CD CE REMARK 470 LYS A 75 NZ REMARK 470 GLU B 2 CG CD OE1 OE2 REMARK 470 LYS B 7 CE NZ REMARK 470 GLU B 10 CD OE1 OE2 REMARK 470 LYS B 13 NZ REMARK 470 GLU B 31 CD OE1 OE2 REMARK 470 LYS B 34 NZ REMARK 470 LYS B 35 CE NZ REMARK 470 LYS B 75 C O CG CD CE NZ 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 B 132 O HOH B 175 2.04 REMARK 500 O HOH A 202 O HOH A 218 2.13 REMARK 500 O HOH A 188 O HOH A 203 2.13 REMARK 500 O HOH A 189 O HOH A 224 2.15 REMARK 500 O HOH A 163 O HOH B 125 2.18 REMARK 500 REMARK 500 REMARK: NULL REMARK 525 REMARK 525 SOLVENT REMARK 525 REMARK 525 THE SOLVENT MOLECULES HAVE CHAIN IDENTIFIERS THAT REMARK 525 INDICATE THE POLYMER CHAIN WITH WHICH THEY ARE MOST REMARK 525 CLOSELY ASSOCIATED. THE REMARK LISTS ALL THE SOLVENT REMARK 525 MOLECULES WHICH ARE MORE THAN 5A AWAY FROM THE REMARK 525 NEAREST POLYMER CHAIN (M = MODEL NUMBER; REMARK 525 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE REMARK 525 NUMBER; I=INSERTION CODE): REMARK 525 REMARK 525 M RES CSSEQI REMARK 525 HOH A 225 DISTANCE = 5.88 ANGSTROMS REMARK 525 HOH A 226 DISTANCE = 6.16 ANGSTROMS REMARK 525 HOH B 224 DISTANCE = 6.31 ANGSTROMS REMARK 525 HOH B 225 DISTANCE = 6.48 ANGSTROMS DBREF 6MSQ A 0 75 PDB 6MSQ 6MSQ 0 75 DBREF 6MSQ B 0 75 PDB 6MSQ 6MSQ 0 75 SEQRES 1 A 76 GLY SER GLU TYR GLU ILE ARG LYS ALA LEU GLU GLU LEU SEQRES 2 A 76 LYS ALA SER THR ALA GLU LEU LYS ARG ALA THR ALA SER SEQRES 3 A 76 LEU ARG ALA ILE THR GLU GLU LEU LYS LYS ASN PRO SER SEQRES 4 A 76 GLU ASP ALA LEU VAL GLU HIS ASN ARG ALA ILE VAL GLU SEQRES 5 A 76 HIS ASN ALA ILE ILE VAL GLU ASN ASN ARG ILE ILE ALA SEQRES 6 A 76 ALA VAL LEU GLU LEU ILE VAL ARG ALA ILE LYS SEQRES 1 B 76 GLY SER GLU TYR GLU ILE ARG LYS ALA LEU GLU GLU LEU SEQRES 2 B 76 LYS ALA SER THR ALA GLU LEU LYS ARG ALA THR ALA SER SEQRES 3 B 76 LEU ARG ALA ILE THR GLU GLU LEU LYS LYS ASN PRO SER SEQRES 4 B 76 GLU ASP ALA LEU VAL GLU HIS ASN ARG ALA ILE VAL GLU SEQRES 5 B 76 HIS ASN ALA ILE ILE VAL GLU ASN ASN ARG ILE ILE ALA SEQRES 6 B 76 ALA VAL LEU GLU LEU ILE VAL ARG ALA ILE LYS FORMUL 3 HOH *251(H2 O) HELIX 1 AA1 GLY A 0 ASN A 36 1 37 HELIX 2 AA2 SER A 38 ILE A 74 1 37 HELIX 3 AA3 SER B 1 ASN B 36 1 36 HELIX 4 AA4 SER B 38 ILE B 74 1 37 CRYST1 50.566 50.566 130.753 90.00 90.00 120.00 P 63 12 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 0.019776 0.011418 0.000000 0.00000 SCALE2 0.000000 0.022835 0.000000 0.00000 SCALE3 0.000000 0.000000 0.007648 0.00000