HEADER DE NOVO PROTEIN 09-JUN-14 4QKR TITLE CRYSTAL STRUCTURE OF 6XTYR/PV2: DE NOVO DESIGNED BETA-TREFOIL TITLE 2 ARCHITECTURE WITH SYMMETRIC PRIMARY STRUCTURE TITLE 3 (L22Y/L44Y/L64Y/L85Y/L108Y/L132Y, PRIMITIVE VERSION 2) COMPND MOL_ID: 1; COMPND 2 MOLECULE: DE NOVO PROTEIN 6XTYR/PV2; COMPND 3 CHAIN: A; COMPND 4 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: SYNTHETIC; SOURCE 3 ORGANISM_TAXID: 32630; SOURCE 4 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 5 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 6 EXPRESSION_SYSTEM_STRAIN: BL21(DE3); SOURCE 7 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 8 EXPRESSION_SYSTEM_PLASMID: PET21A(+); SOURCE 9 OTHER_DETAILS: SYNTHETIC SEQUENCE DERIVED FROM HUMAN ACIDIC SOURCE 10 FIBROBLAST GROWTH FACTOR WITH SYMMETRIC DECONSTRUCTION METHOD AND SOURCE 11 ENRICHED FOR PRE-BIOTIC AMINO ACIDS. KEYWDS SIMPLIFIED PROTEIN DESIGN, PREBIOTIC PROTEIN, BETA-TREFOIL, DE NOVO KEYWDS 2 PROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR L.M.LONGO,M.BLABER,C.A.TENORIO REVDAT 3 28-FEB-24 4QKR 1 REMARK REVDAT 2 22-NOV-17 4QKR 1 REMARK REVDAT 1 14-JAN-15 4QKR 0 JRNL AUTH L.M.LONGO,C.A.TENORIO,O.S.KUMRU,C.R.MIDDAUGH,M.BLABER JRNL TITL A SINGLE AROMATIC CORE MUTATION CONVERTS A DESIGNED JRNL TITL 2 "PRIMITIVE" PROTEIN FROM HALOPHILE TO MESOPHILE FOLDING. JRNL REF PROTEIN SCI. V. 24 27 2015 JRNL REFN ISSN 0961-8368 JRNL PMID 25297559 JRNL DOI 10.1002/PRO.2580 REMARK 2 REMARK 2 RESOLUTION. 1.75 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.7.3_928 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) : 1.75 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 33.82 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.370 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.4 REMARK 3 NUMBER OF REFLECTIONS : 11651 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.188 REMARK 3 R VALUE (WORKING SET) : 0.187 REMARK 3 FREE R VALUE : 0.216 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.000 REMARK 3 FREE R VALUE TEST SET COUNT : 583 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 33.8303 - 2.7713 1.00 2898 153 0.1712 0.1799 REMARK 3 2 2.7713 - 2.1998 1.00 2776 146 0.1927 0.2356 REMARK 3 3 2.1998 - 1.9218 1.00 2721 144 0.1950 0.2591 REMARK 3 4 1.9218 - 1.7461 0.98 2673 140 0.2596 0.2994 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : FLAT BULK SOLVENT MODEL REMARK 3 SOLVENT RADIUS : 0.80 REMARK 3 SHRINKAGE RADIUS : 0.47 REMARK 3 K_SOL : 0.37 REMARK 3 B_SOL : 43.83 REMARK 3 REMARK 3 ERROR ESTIMATES. REMARK 3 COORDINATE ERROR (MAXIMUM-LIKELIHOOD BASED) : 0.220 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 21.300 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 26.29 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -0.45530 REMARK 3 B22 (A**2) : -5.20790 REMARK 3 B33 (A**2) : 5.66320 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : 0.00000 REMARK 3 B23 (A**2) : 0.00000 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 1053 REMARK 3 ANGLE : 1.101 1441 REMARK 3 CHIRALITY : 0.074 154 REMARK 3 PLANARITY : 0.006 204 REMARK 3 DIHEDRAL : 15.060 427 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 4QKR COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 16-JUN-14. REMARK 100 THE DEPOSITION ID IS D_1000086178. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 20-MAY-13 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 8.0 REMARK 200 NUMBER OF CRYSTALS USED : 1 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 RUH3R REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.541 REMARK 200 MONOCHROMATOR : MULTI-LAYER MIRRORS REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : IMAGE PLATE REMARK 200 DETECTOR MANUFACTURER : RIGAKU RAXIS IV++ REMARK 200 INTENSITY-INTEGRATION SOFTWARE : DENZO REMARK 200 DATA SCALING SOFTWARE : SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 11690 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.746 REMARK 200 RESOLUTION RANGE LOW (A) : 40.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.6 REMARK 200 DATA REDUNDANCY : 7.300 REMARK 200 R MERGE (I) : 0.05200 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 18.1000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.75 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.81 REMARK 200 COMPLETENESS FOR SHELL (%) : 98.3 REMARK 200 DATA REDUNDANCY IN SHELL : 5.90 REMARK 200 R MERGE FOR SHELL (I) : 0.31100 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : NULL REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: NULL REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 34.62 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 1.88 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 30% PEG 8,000, 0.1 M IMIDAZOLE HCL, REMARK 280 0.2 M NACL, PH 8.0, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE REMARK 280 298K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 21 21 21 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X+1/2,-Y,Z+1/2 REMARK 290 3555 -X,Y+1/2,-Z+1/2 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 17.38150 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 33.82400 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 23.39600 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 33.82400 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 17.38150 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 23.39600 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 HIS A 5 REMARK 465 HIS A 6 REMARK 465 HIS A 7 REMARK 465 HIS A 8 REMARK 465 GLY A 138 REMARK 465 ASN A 139 REMARK 465 GLY A 140 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 94 O HOH A 414 2.07 REMARK 500 OG SER A 58 O HOH A 385 2.11 REMARK 500 O HOH A 405 O HOH A 410 2.17 REMARK 500 OG SER A 79 O HOH A 398 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 NH2 ARG A 35 O GLY A 52 3554 2.15 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 PRO A 136 C - N - CA ANGL. DEV. = 11.7 DEGREES 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 IMD A 200 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 4D8H RELATED DB: PDB REMARK 900 RELATED ID: 4QKS RELATED DB: PDB DBREF 4QKR A 5 140 PDB 4QKR 4QKR 5 140 SEQRES 1 A 132 HIS HIS HIS HIS HIS HIS GLU VAL LEU LEU ARG SER THR SEQRES 2 A 132 GLU THR GLY GLN TYR LEU ARG ILE ASN PRO ASP GLY THR SEQRES 3 A 132 VAL ASP GLY THR ARG ASP ARG SER ASP PRO GLY ILE GLN SEQRES 4 A 132 TYR GLN ILE SER PRO GLU GLY ASN GLY GLU VAL LEU LEU SEQRES 5 A 132 ARG SER THR GLU THR GLY GLN TYR LEU ARG ILE ASN PRO SEQRES 6 A 132 ASP GLY THR VAL ASP GLY THR ARG ASP ARG SER ASP PRO SEQRES 7 A 132 GLY ILE GLN TYR GLN ILE SER PRO GLU GLY ASN GLY GLU SEQRES 8 A 132 VAL LEU LEU ARG SER THR GLU THR GLY GLN TYR LEU ARG SEQRES 9 A 132 ILE ASN PRO ASP GLY THR VAL ASP GLY THR ARG ASP ARG SEQRES 10 A 132 SER ASP PRO GLY ILE GLN TYR GLN ILE SER PRO GLU GLY SEQRES 11 A 132 ASN GLY HET IMD A 200 5 HETNAM IMD IMIDAZOLE FORMUL 2 IMD C3 H5 N2 1+ FORMUL 3 HOH *116(H2 O) HELIX 1 1 ASP A 39 GLY A 41 5 3 HELIX 2 2 ASP A 127 GLY A 129 5 3 SHEET 1 A 7 VAL A 12 SER A 16 0 SHEET 2 A 7 GLN A 43 GLY A 50 -1 O TYR A 44 N VAL A 12 SHEET 3 A 7 GLU A 53 SER A 58 -1 O LEU A 55 N SER A 47 SHEET 4 A 7 TYR A 85 GLY A 91 -1 O TYR A 85 N VAL A 54 SHEET 5 A 7 GLU A 94 SER A 99 -1 O GLU A 94 N GLU A 90 SHEET 6 A 7 GLN A 131 PRO A 136 -1 O TYR A 132 N VAL A 95 SHEET 7 A 7 VAL A 12 SER A 16 -1 N ARG A 15 O GLN A 133 SHEET 1 B 2 TYR A 22 ILE A 25 0 SHEET 2 B 2 VAL A 31 THR A 34 -1 O THR A 34 N TYR A 22 SHEET 1 C 2 TYR A 64 ILE A 67 0 SHEET 2 C 2 VAL A 73 THR A 76 -1 O THR A 76 N TYR A 64 SHEET 1 D 2 TYR A 108 ILE A 111 0 SHEET 2 D 2 VAL A 117 THR A 123 -1 O THR A 123 N TYR A 108 SITE 1 AC1 6 HIS A 10 VAL A 12 GLU A 18 PRO A 113 SITE 2 AC1 6 HOH A 306 HOH A 333 CRYST1 34.763 46.792 67.648 90.00 90.00 90.00 P 21 21 21 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 0.028766 0.000000 0.000000 0.00000 SCALE2 0.000000 0.021371 0.000000 0.00000 SCALE3 0.000000 0.000000 0.014782 0.00000