HEADER DE NOVO PROTEIN 30-NOV-25 9ZEM TITLE HELISCREW4 COMPND MOL_ID: 1; COMPND 2 MOLECULE: HELISCREW4; COMPND 3 CHAIN: A, B; COMPND 4 ENGINEERED: YES; COMPND 5 OTHER_DETAILS: HELISCREW4 SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: SYNTHETIC CONSTRUCT; SOURCE 3 ORGANISM_TAXID: 32630; SOURCE 4 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21(DE3); SOURCE 5 EXPRESSION_SYSTEM_TAXID: 469008 KEYWDS HELISCREW, DE NOVO PROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR H.YANG,W.F.DEGRADO REVDAT 1 17-JUN-26 9ZEM 0 JRNL AUTH R.YANG,H.YANG,R.KORMOS,A.DAVYDENKO,Z.MAWALDI,D.MYERSCOUGH, JRNL AUTH 2 Y.WU,W.F.DEGRADO JRNL TITL THE EMERGENCE OF NOVEL VERSUS KNOWN THREE-DIMENSIONAL JRNL TITL 2 STRUCTURES FROM RANDOM SEQUENCES. JRNL REF TO BE PUBLISHED JRNL REFN REMARK 2 REMARK 2 RESOLUTION. 2.20 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.21.2_5419 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) : 2.20 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 45.69 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.380 REMARK 3 COMPLETENESS FOR RANGE (%) : 92.5 REMARK 3 NUMBER OF REFLECTIONS : 19429 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.201 REMARK 3 R VALUE (WORKING SET) : 0.197 REMARK 3 FREE R VALUE : 0.237 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 10.040 REMARK 3 FREE R VALUE TEST SET COUNT : 1951 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 45.6900 - 5.3000 0.93 1259 139 0.2029 0.2214 REMARK 3 2 5.3000 - 4.2100 0.96 1290 143 0.1873 0.2322 REMARK 3 3 4.2100 - 3.6800 0.94 1264 142 0.1558 0.1943 REMARK 3 4 3.6800 - 3.3400 0.87 1197 133 0.1865 0.2224 REMARK 3 5 3.3400 - 3.1000 0.94 1246 140 0.2031 0.2018 REMARK 3 6 3.1000 - 2.9200 0.94 1269 144 0.2171 0.2641 REMARK 3 7 2.9200 - 2.7700 0.95 1305 146 0.1971 0.2170 REMARK 3 8 2.7700 - 2.6500 0.94 1246 139 0.1964 0.2394 REMARK 3 9 2.6500 - 2.5500 0.94 1277 144 0.1873 0.2445 REMARK 3 10 2.5500 - 2.4600 0.84 1138 125 0.2143 0.2791 REMARK 3 11 2.4600 - 2.3800 0.93 1269 140 0.2121 0.2898 REMARK 3 12 2.3800 - 2.3200 0.92 1199 134 0.2144 0.2672 REMARK 3 13 2.3200 - 2.2600 0.92 1287 146 0.2388 0.2674 REMARK 3 14 2.2600 - 2.2000 0.93 1232 136 0.2290 0.3307 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) : 0.227 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 25.249 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 18.54 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 24.84 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 : 0.008 1746 REMARK 3 ANGLE : 1.076 2396 REMARK 3 CHIRALITY : 0.045 302 REMARK 3 PLANARITY : 0.022 320 REMARK 3 DIHEDRAL : 5.169 242 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 9ZEM COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 01-DEC-25. REMARK 100 THE DEPOSITION ID IS D_1000302725. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 26-OCT-25 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 : APS REMARK 200 BEAMLINE : 24-ID-E REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.980 REMARK 200 MONOCHROMATOR : SI(220) REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS EIGER X 16M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : RAPD REMARK 200 DATA SCALING SOFTWARE : RAPD REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 68979 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.046 REMARK 200 RESOLUTION RANGE LOW (A) : 45.690 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 92.4 REMARK 200 DATA REDUNDANCY : 5.400 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 5.2900 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.05 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.09 REMARK 200 COMPLETENESS FOR SHELL (%) : 91.2 REMARK 200 DATA REDUNDANCY IN SHELL : 5.60 REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 3.170 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 (%): 42.46 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.14 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 1.8 M AMMONIUM CITRATE TRIBASIC, PH REMARK 280 7.0, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 293K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 1 21 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,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 31.31000 REMARK 290 SMTRY3 2 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: 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 ALA A 1 REMARK 465 GLU A 2 REMARK 465 GLY A 120 REMARK 465 ALA B 1 REMARK 465 GLU B 2 REMARK 465 GLY B 120 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 231 O HOH B 264 1.88 REMARK 500 OE2 GLU A 89 O HOH A 201 2.07 REMARK 500 O ALA A 108 O HOH A 202 2.11 REMARK 500 O HOH A 206 O HOH A 268 2.11 REMARK 500 OE1 GLU A 9 O HOH A 203 2.11 REMARK 500 O HOH A 229 O HOH A 233 2.13 REMARK 500 O HOH B 255 O HOH B 274 2.14 REMARK 500 O HOH A 267 O HOH B 207 2.14 REMARK 500 O LEU B 38 O HOH B 201 2.15 REMARK 500 O MET B 62 O HOH B 202 2.15 REMARK 500 O HOH A 219 O HOH A 256 2.15 REMARK 500 O HOH A 272 O HOH B 265 2.17 REMARK 500 O HOH B 249 O HOH B 270 2.17 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CLOSE CONTACTS REMARK 500 REMARK 500 THE FOLLOWING ATOMS THAT ARE RELATED BY CRYSTALLOGRAPHIC REMARK 500 SYMMETRY ARE IN CLOSE CONTACT. AN ATOM LOCATED WITHIN 0.15 REMARK 500 ANGSTROMS OF A SYMMETRY RELATED ATOM IS ASSUMED TO BE ON A REMARK 500 SPECIAL POSITION AND IS, THEREFORE, LISTED IN REMARK 375 REMARK 500 INSTEAD OF REMARK 500. ATOMS WITH NON-BLANK ALTERNATE REMARK 500 LOCATION INDICATORS ARE NOT INCLUDED IN THE CALCULATIONS. REMARK 500 REMARK 500 DISTANCE CUTOFF: REMARK 500 2.2 ANGSTROMS FOR CONTACTS NOT INVOLVING HYDROGEN ATOMS REMARK 500 1.6 ANGSTROMS FOR CONTACTS INVOLVING HYDROGEN ATOMS REMARK 500 REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI SSYMOP DISTANCE REMARK 500 O HOH A 255 O HOH B 244 1554 2.16 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: COVALENT BOND ANGLES REMARK 500 REMARK 500 THE STEREOCHEMICAL PARAMETERS OF THE FOLLOWING RESIDUES REMARK 500 HAVE VALUES WHICH DEVIATE FROM EXPECTED VALUES BY MORE REMARK 500 THAN 6*RMSD (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 500 IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 STANDARD TABLE: REMARK 500 FORMAT: (10X,I3,1X,A3,1X,A1,I4,A1,3(1X,A4,2X),12X,F5.1) REMARK 500 REMARK 500 EXPECTED VALUES PROTEIN: ENGH AND HUBER, 1999 REMARK 500 EXPECTED VALUES NUCLEIC ACID: CLOWNEY ET AL 1996 REMARK 500 REMARK 500 M RES CSSEQI ATM1 ATM2 ATM3 REMARK 500 ARG B 21 CG - CD - NE ANGL. DEV. = -18.6 DEGREES REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: PLANAR GROUPS REMARK 500 REMARK 500 PLANAR GROUPS IN THE FOLLOWING RESIDUES HAVE A TOTAL REMARK 500 RMS DISTANCE OF ALL ATOMS FROM THE BEST-FIT PLANE REMARK 500 BY MORE THAN AN EXPECTED VALUE OF 6*RMSD, WITH AN REMARK 500 RMSD 0.02 ANGSTROMS, OR AT LEAST ONE ATOM HAS REMARK 500 AN RMSD GREATER THAN THIS VALUE REMARK 500 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 500 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 M RES CSSEQI RMS TYPE REMARK 500 ARG A 115 0.09 SIDE CHAIN REMARK 500 ARG A 117 0.17 SIDE CHAIN REMARK 500 REMARK 500 REMARK: NULL DBREF 9ZEM A 1 120 PDB 9ZEM 9ZEM 1 120 DBREF 9ZEM B 1 120 PDB 9ZEM 9ZEM 1 120 SEQRES 1 A 120 ALA GLU VAL ALA ALA LEU THR PRO GLU GLN ILE ALA ALA SEQRES 2 A 120 LEU SER VAL ASP GLU ILE ALA ARG LEU SER PRO ASP GLN SEQRES 3 A 120 PHE ALA ALA LEU THR PRO GLU GLN ILE ALA ALA LEU THR SEQRES 4 A 120 PRO GLU GLN VAL ALA ARG LEU SER PRO GLU LYS ILE ALA SEQRES 5 A 120 ALA LEU SER PRO ASP LYS ILE ALA ALA MET THR PRO GLU SEQRES 6 A 120 GLN VAL ALA ALA LEU THR PRO GLU GLN PHE ALA ALA LEU SEQRES 7 A 120 SER PRO ASP LYS ILE ALA ALA LEU THR PRO GLU GLN ILE SEQRES 8 A 120 ALA ALA VAL SER ASP GLU THR LEU ARG ALA LEU SER PRO SEQRES 9 A 120 GLU LYS GLN ALA ALA LEU PRO PRO GLU VAL ARG ALA ARG SEQRES 10 A 120 LEU ALA GLY SEQRES 1 B 120 ALA GLU VAL ALA ALA LEU THR PRO GLU GLN ILE ALA ALA SEQRES 2 B 120 LEU SER VAL ASP GLU ILE ALA ARG LEU SER PRO ASP GLN SEQRES 3 B 120 PHE ALA ALA LEU THR PRO GLU GLN ILE ALA ALA LEU THR SEQRES 4 B 120 PRO GLU GLN VAL ALA ARG LEU SER PRO GLU LYS ILE ALA SEQRES 5 B 120 ALA LEU SER PRO ASP LYS ILE ALA ALA MET THR PRO GLU SEQRES 6 B 120 GLN VAL ALA ALA LEU THR PRO GLU GLN PHE ALA ALA LEU SEQRES 7 B 120 SER PRO ASP LYS ILE ALA ALA LEU THR PRO GLU GLN ILE SEQRES 8 B 120 ALA ALA VAL SER ASP GLU THR LEU ARG ALA LEU SER PRO SEQRES 9 B 120 GLU LYS GLN ALA ALA LEU PRO PRO GLU VAL ARG ALA ARG SEQRES 10 B 120 LEU ALA GLY FORMUL 3 HOH *151(H2 O) HELIX 1 AA1 THR A 7 LEU A 14 1 8 HELIX 2 AA2 SER A 15 LEU A 22 1 8 HELIX 3 AA3 SER A 23 ALA A 28 1 6 HELIX 4 AA4 THR A 31 ALA A 37 1 7 HELIX 5 AA5 THR A 39 ARG A 45 1 7 HELIX 6 AA6 SER A 47 ALA A 53 1 7 HELIX 7 AA7 SER A 55 ALA A 60 1 6 HELIX 8 AA8 THR A 63 LEU A 70 1 8 HELIX 9 AA9 THR A 71 ALA A 76 1 6 HELIX 10 AB1 SER A 79 LEU A 86 1 8 HELIX 11 AB2 THR A 87 ALA A 92 1 6 HELIX 12 AB3 SER A 95 ALA A 101 1 7 HELIX 13 AB4 SER A 103 ALA A 109 1 7 HELIX 14 AB5 PRO A 111 LEU A 118 1 8 HELIX 15 AB6 THR B 7 ALA B 13 1 7 HELIX 16 AB7 SER B 15 ARG B 21 1 7 HELIX 17 AB8 SER B 23 ALA B 28 1 6 HELIX 18 AB9 THR B 31 ALA B 37 1 7 HELIX 19 AC1 THR B 39 LEU B 46 1 8 HELIX 20 AC2 SER B 47 ALA B 53 1 7 HELIX 21 AC3 SER B 55 ALA B 60 1 6 HELIX 22 AC4 THR B 63 ALA B 68 1 6 HELIX 23 AC5 THR B 71 LEU B 78 1 8 HELIX 24 AC6 SER B 79 ALA B 85 1 7 HELIX 25 AC7 THR B 87 ALA B 92 1 6 HELIX 26 AC8 SER B 95 LEU B 102 1 8 HELIX 27 AC9 SER B 103 ALA B 108 1 6 HELIX 28 AD1 PRO B 111 ALA B 119 1 9 CRYST1 37.339 62.620 45.980 90.00 96.42 90.00 P 1 21 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 0.026782 0.000000 0.003014 0.00000 SCALE2 0.000000 0.015969 0.000000 0.00000 SCALE3 0.000000 0.000000 0.021886 0.00000 MASTER 282 0 0 28 0 0 0 6 1869 2 0 20 END