HEADER DE NOVO PROTEIN 19-AUG-18 6EGC TITLE SINGLE-CHAIN VERSION OF 2L4HC2_23 (PDB 5J0K) COMPND MOL_ID: 1; COMPND 2 MOLECULE: SC_2L4HC2_23; COMPND 3 CHAIN: A; 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 COMPUTATIONAL DESIGN, HELICAL BUNDLE, DE NOVO PROTEIN, COILED-COIL EXPDTA X-RAY DIFFRACTION AUTHOR M.J.BICK,Z.CHEN,F.DIMAIO REVDAT 5 03-APR-24 6EGC 1 REMARK REVDAT 4 13-MAR-24 6EGC 1 REMARK REVDAT 3 01-JAN-20 6EGC 1 REMARK REVDAT 2 26-JUN-19 6EGC 1 JRNL REVDAT 1 29-MAY-19 6EGC 0 JRNL AUTH Z.CHEN,M.C.JOHNSON,J.CHEN,M.J.BICK,S.E.BOYKEN,B.LIN, JRNL AUTH 2 J.J.DE YOREO,J.M.KOLLMAN,D.BAKER,F.DIMAIO JRNL TITL SELF-ASSEMBLING 2D ARRAYS WITH DE NOVO PROTEIN BUILDING JRNL TITL 2 BLOCKS. JRNL REF J.AM.CHEM.SOC. V. 141 8891 2019 JRNL REFN ESSN 1520-5126 JRNL PMID 31050411 JRNL DOI 10.1021/JACS.9B01978 REMARK 2 REMARK 2 RESOLUTION. 1.74 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) : 1.74 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 22.52 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 92.1 REMARK 3 NUMBER OF REFLECTIONS : 15269 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.230 REMARK 3 R VALUE (WORKING SET) : 0.227 REMARK 3 FREE R VALUE : 0.266 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 9.570 REMARK 3 FREE R VALUE TEST SET COUNT : 1461 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 22.5219 - 3.7437 0.91 1403 146 0.2178 0.2435 REMARK 3 2 3.7437 - 2.9736 1.00 1506 159 0.2193 0.2738 REMARK 3 3 2.9736 - 2.5984 1.00 1493 162 0.2321 0.2527 REMARK 3 4 2.5984 - 2.3611 0.99 1490 162 0.2179 0.2600 REMARK 3 5 2.3611 - 2.1920 0.99 1478 149 0.2186 0.2619 REMARK 3 6 2.1920 - 2.0629 0.97 1448 150 0.2237 0.3179 REMARK 3 7 2.0629 - 1.9596 0.94 1395 153 0.2535 0.2851 REMARK 3 8 1.9596 - 1.8743 0.86 1271 133 0.2751 0.3414 REMARK 3 9 1.8743 - 1.8022 0.80 1204 126 0.3235 0.3603 REMARK 3 10 1.8022 - 1.7401 0.76 1120 121 0.3869 0.4204 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) : 0.240 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 32.840 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 29.00 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 58.90 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 : 0.019 1135 REMARK 3 ANGLE : 1.448 1522 REMARK 3 CHIRALITY : 0.072 185 REMARK 3 PLANARITY : 0.008 199 REMARK 3 DIHEDRAL : 14.404 735 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : 4 REMARK 3 TLS GROUP : 1 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 1 THROUGH 35 ) REMARK 3 ORIGIN FOR THE GROUP (A): 7.2772 26.1110 1.7753 REMARK 3 T TENSOR REMARK 3 T11: 0.4004 T22: 0.4075 REMARK 3 T33: 0.3999 T12: 0.0513 REMARK 3 T13: -0.0659 T23: -0.0046 REMARK 3 L TENSOR REMARK 3 L11: 4.0929 L22: 0.8143 REMARK 3 L33: 8.2398 L12: -0.7142 REMARK 3 L13: -1.8816 L23: 1.3192 REMARK 3 S TENSOR REMARK 3 S11: 0.3304 S12: 0.7844 S13: 0.2886 REMARK 3 S21: -0.2647 S22: -0.3466 S23: 0.1158 REMARK 3 S31: -0.5885 S32: -0.8759 S33: -0.1795 REMARK 3 TLS GROUP : 2 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 36 THROUGH 73 ) REMARK 3 ORIGIN FOR THE GROUP (A): 6.7535 18.7613 6.6441 REMARK 3 T TENSOR REMARK 3 T11: 0.3319 T22: 0.3528 REMARK 3 T33: 0.3611 T12: -0.0432 REMARK 3 T13: -0.0267 T23: -0.0535 REMARK 3 L TENSOR REMARK 3 L11: 8.5869 L22: 1.9029 REMARK 3 L33: 4.7551 L12: 0.4670 REMARK 3 L13: -2.8900 L23: -0.5470 REMARK 3 S TENSOR REMARK 3 S11: -0.0177 S12: -0.6264 S13: -0.4976 REMARK 3 S21: 0.1630 S22: -0.1920 S23: 0.2237 REMARK 3 S31: 0.1743 S32: -0.2752 S33: 0.4380 REMARK 3 TLS GROUP : 3 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 79 THROUGH 112 ) REMARK 3 ORIGIN FOR THE GROUP (A): 15.7223 21.7843 12.5267 REMARK 3 T TENSOR REMARK 3 T11: 0.3925 T22: 0.4456 REMARK 3 T33: 0.3478 T12: -0.0381 REMARK 3 T13: -0.0704 T23: 0.0514 REMARK 3 L TENSOR REMARK 3 L11: 3.7449 L22: 2.0943 REMARK 3 L33: 7.1105 L12: 1.0898 REMARK 3 L13: -2.2556 L23: -1.6744 REMARK 3 S TENSOR REMARK 3 S11: 0.6286 S12: -1.4834 S13: -0.5700 REMARK 3 S21: 0.5114 S22: -0.7572 S23: -0.3195 REMARK 3 S31: -0.2002 S32: 1.0400 S33: 0.1760 REMARK 3 TLS GROUP : 4 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 113 THROUGH 151 ) REMARK 3 ORIGIN FOR THE GROUP (A): 11.5684 29.3496 11.0825 REMARK 3 T TENSOR REMARK 3 T11: 0.3614 T22: 0.3528 REMARK 3 T33: 0.3129 T12: -0.0407 REMARK 3 T13: -0.0373 T23: -0.0507 REMARK 3 L TENSOR REMARK 3 L11: 5.9563 L22: 1.8233 REMARK 3 L33: 7.7200 L12: -0.1048 REMARK 3 L13: -3.9078 L23: 0.1820 REMARK 3 S TENSOR REMARK 3 S11: 0.3056 S12: -0.3518 S13: 0.3726 REMARK 3 S21: 0.2587 S22: -0.1946 S23: 0.0775 REMARK 3 S31: -0.3192 S32: -0.2349 S33: -0.2005 REMARK 3 REMARK 3 NCS DETAILS REMARK 3 NUMBER OF NCS GROUPS : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: ITERATIVE ROUNDS OF MODEL BUILDING IN REMARK 3 COOT AND REFINEMENT IN PHENIX. REMARK 4 REMARK 4 6EGC COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 20-AUG-18. REMARK 100 THE DEPOSITION ID IS D_1000236198. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 09-MAR-16 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 8.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : ALS REMARK 200 BEAMLINE : 8.2.1 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.999978 REMARK 200 MONOCHROMATOR : DOUBLE-CRYSTAL SI(111) AND REMARK 200 MULTILAYER REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 315R REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 V715 REMARK 200 DATA SCALING SOFTWARE : HKL-2000 V715 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 20818 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.470 REMARK 200 RESOLUTION RANGE LOW (A) : 50.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 75.5 REMARK 200 DATA REDUNDANCY : 3.400 REMARK 200 R MERGE (I) : 0.05500 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 7.3000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.47 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.50 REMARK 200 COMPLETENESS FOR SHELL (%) : 5.8 REMARK 200 DATA REDUNDANCY IN SHELL : 1.10 REMARK 200 R MERGE FOR SHELL (I) : 2.72300 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 0.150 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: PHASER 2.8.2 REMARK 200 STARTING MODEL: COMPUTATIONAL DESIGN MODEL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 43.72 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.19 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: MOLECULAR DIMENSIONS MORPHEUS H9 (0.1M REMARK 280 AMINO ACIDS, 0.1M BUFFER SYSTEM 3 PH 8.5, 50% (V/V) PRECIPITANT REMARK 280 MIX 1), VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 291.15K 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 24.68000 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: 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 GLY A -3 REMARK 465 SER A -2 REMARK 465 HIS A -1 REMARK 465 MET A 0 REMARK 465 GLN A 75 REMARK 465 GLY A 76 REMARK 465 PRO A 77 REMARK 465 PRO A 78 REMARK 465 ASP A 152 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 THR A 1 N CB OG1 CG2 REMARK 470 ARG A 2 CG CD NE CZ NH1 NH2 REMARK 470 GLU A 4 CD OE1 OE2 REMARK 470 GLU A 18 CD OE1 OE2 REMARK 470 LYS A 21 CG CD CE NZ REMARK 470 GLU A 25 CD OE1 OE2 REMARK 470 ARG A 28 NE CZ NH1 NH2 REMARK 470 LEU A 33 CG CD1 CD2 REMARK 470 GLN A 34 CG CD OE1 NE2 REMARK 470 ARG A 35 CZ NH1 NH2 REMARK 470 SER A 38 OG REMARK 470 ARG A 44 CG CD NE CZ NH1 NH2 REMARK 470 ARG A 48 CG CD NE CZ NH1 NH2 REMARK 470 LYS A 51 CD CE NZ REMARK 470 GLU A 52 CG CD OE1 OE2 REMARK 470 GLU A 56 CG CD OE1 OE2 REMARK 470 LYS A 59 CD CE NZ REMARK 470 GLU A 69 CD OE1 OE2 REMARK 470 ARG A 73 CD NE CZ NH1 NH2 REMARK 470 GLN A 74 CG CD OE1 NE2 REMARK 470 GLU A 95 CD OE1 OE2 REMARK 470 LYS A 98 CG CD CE NZ REMARK 470 ARG A 105 CZ NH1 NH2 REMARK 470 LEU A 110 CG CD1 CD2 REMARK 470 GLN A 111 CG CD OE1 NE2 REMARK 470 ARG A 112 CD NE CZ NH1 NH2 REMARK 470 GLU A 113 CG CD OE1 OE2 REMARK 470 SER A 115 OG REMARK 470 ARG A 121 CG CD NE CZ NH1 NH2 REMARK 470 GLU A 122 CG CD OE1 OE2 REMARK 470 ARG A 125 CD NE CZ NH1 NH2 REMARK 470 LYS A 128 CD CE NZ REMARK 470 GLU A 129 CD OE1 OE2 REMARK 470 LYS A 136 CD CE NZ REMARK 470 LYS A 142 CD CE NZ REMARK 470 GLU A 146 CD OE1 OE2 REMARK 470 ARG A 150 NE CZ NH1 NH2 REMARK 470 GLN A 151 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 OE2 GLU A 10 HZ2 LYS A 149 1.59 REMARK 500 OE2 GLU A 140 O HOH A 201 2.07 REMARK 500 OE2 GLU A 15 O HOH A 202 2.16 REMARK 500 REMARK 500 REMARK: NULL DBREF 6EGC A -3 152 PDB 6EGC 6EGC -3 152 SEQRES 1 A 156 GLY SER HIS MET THR ARG THR GLU ILE ILE ARG GLU LEU SEQRES 2 A 156 GLU ARG SER LEU ARG GLU GLN GLU GLU LEU ALA LYS ARG SEQRES 3 A 156 LEU LYS GLU LEU LEU ARG GLU LEU GLU ARG LEU GLN ARG SEQRES 4 A 156 GLU GLY SER SER ASP GLU ASP VAL ARG GLU LEU LEU ARG SEQRES 5 A 156 GLU ILE LYS GLU LEU VAL GLU GLU ILE GLU LYS LEU ALA SEQRES 6 A 156 ARG GLU GLN LYS TYR LEU VAL GLU GLU LEU LYS ARG GLN SEQRES 7 A 156 GLN GLY PRO PRO GLY ASN GLU ILE ILE ARG GLU LEU GLU SEQRES 8 A 156 ARG SER LEU ARG GLU GLN GLU GLU LEU ALA LYS ARG LEU SEQRES 9 A 156 LYS GLU LEU LEU ARG GLU LEU GLU ARG LEU GLN ARG GLU SEQRES 10 A 156 GLY SER SER ASP GLU ASP VAL ARG GLU LEU LEU ARG GLU SEQRES 11 A 156 ILE LYS GLU LEU VAL GLU GLU ILE GLU LYS LEU ALA ARG SEQRES 12 A 156 GLU GLN LYS TYR LEU VAL GLU GLU LEU LYS ARG GLN ASP FORMUL 2 HOH *47(H2 O) HELIX 1 AA1 THR A 1 GLY A 37 1 37 HELIX 2 AA2 SER A 39 GLN A 74 1 36 HELIX 3 AA3 ASN A 80 GLY A 114 1 35 HELIX 4 AA4 SER A 116 GLN A 151 1 36 CRYST1 41.253 49.360 41.239 90.00 104.30 90.00 P 1 21 1 2 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 0.024241 0.000000 0.006180 0.00000 SCALE2 0.000000 0.020259 0.000000 0.00000 SCALE3 0.000000 0.000000 0.025025 0.00000