HEADER DE NOVO PROTEIN 09-JUN-14 4QKS TITLE CRYSTAL STRUCTURE OF 6XTRP/PV2: DE NOVO DESIGNED BETA-TREFOIL TITLE 2 ARCHITECTURE WITH SYMMETRIC PRIMARY STRUCTURE TITLE 3 (L22W/L44W/L64W/L85W/L108W/L132W HIS PRIMITIVE VERSION 2) COMPND MOL_ID: 1; COMPND 2 MOLECULE: DE NOVO PROTEIN 6XTRP/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,C.A.TENORIO,M.BLABER REVDAT 2 28-FEB-24 4QKS 1 REMARK REVDAT 1 14-JAN-15 4QKS 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. 1.70 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 : MLHL REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.70 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 39.05 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 2.010 REMARK 3 COMPLETENESS FOR RANGE (%) : 95.3 REMARK 3 NUMBER OF REFLECTIONS : 17307 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.197 REMARK 3 R VALUE (WORKING SET) : 0.195 REMARK 3 FREE R VALUE : 0.232 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.920 REMARK 3 FREE R VALUE TEST SET COUNT : 852 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 39.0554 - 3.0889 0.95 2856 151 0.2026 0.2253 REMARK 3 2 3.0889 - 2.4519 0.99 2866 143 0.1932 0.2440 REMARK 3 3 2.4519 - 2.1420 0.99 2829 147 0.1743 0.2106 REMARK 3 4 2.1420 - 1.9461 0.98 2775 142 0.1640 0.2209 REMARK 3 5 1.9461 - 1.8066 0.95 2683 146 0.1853 0.2270 REMARK 3 6 1.8066 - 1.7001 0.87 2446 123 0.3171 0.3722 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 : 0.86 REMARK 3 K_SOL : 0.40 REMARK 3 B_SOL : 40.00 REMARK 3 REMARK 3 ERROR ESTIMATES. REMARK 3 COORDINATE ERROR (MAXIMUM-LIKELIHOOD BASED) : 0.240 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 17.560 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 25.79 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 26.75 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 0.00000 REMARK 3 B22 (A**2) : 0.00000 REMARK 3 B33 (A**2) : 0.00000 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 1041 REMARK 3 ANGLE : 1.035 1425 REMARK 3 CHIRALITY : 0.063 148 REMARK 3 PLANARITY : 0.004 195 REMARK 3 DIHEDRAL : 14.607 403 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 4QKS 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_1000086179. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 17-MAY-13 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 7.0 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 : OSMIC CONFOCAL MIRROS 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 : NULL REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 17987 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.700 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 (%) : 98.8 REMARK 200 DATA REDUNDANCY : 7.500 REMARK 200 R MERGE (I) : 0.07600 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : NULL REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : NULL REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : NULL REMARK 200 COMPLETENESS FOR SHELL (%) : NULL REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : NULL 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 (%): 54.39 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.70 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 1.4 M (NH4)2SO4, 0.1 M TRIS, 0.07 M REMARK 280 LI2SO4, PH 7.0, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 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 23.56900 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 34.84550 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 24.23550 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 34.84550 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 23.56900 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 24.23550 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 HIS A 9 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 O PRO A 27 O HOH A 423 2.15 REMARK 500 O HOH A 331 O HOH A 338 2.17 REMARK 500 OE1 GLU A 101 O HOH A 344 2.18 REMARK 500 REMARK 500 REMARK: NULL 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 ASP A 118 -154.23 -150.79 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 TRS A 200 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SO4 A 201 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 4D8H RELATED DB: PDB REMARK 900 RELATED ID: 4QKR RELATED DB: PDB DBREF 4QKS A 5 140 PDB 4QKS 4QKS 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 TRP 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 TRP GLN ILE SER PRO GLU GLY ASN GLY GLU VAL LEU LEU SEQRES 5 A 132 ARG SER THR GLU THR GLY GLN TRP 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 TRP GLN ILE SER PRO GLU GLY ASN GLY GLU SEQRES 8 A 132 VAL LEU LEU ARG SER THR GLU THR GLY GLN TRP 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 TRP GLN ILE SER PRO GLU GLY SEQRES 11 A 132 ASN GLY HET TRS A 200 8 HET SO4 A 201 5 HETNAM TRS 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL HETNAM SO4 SULFATE ION HETSYN TRS TRIS BUFFER FORMUL 2 TRS C4 H12 N O3 1+ FORMUL 3 SO4 O4 S 2- FORMUL 4 HOH *136(H2 O) HELIX 1 1 ASP A 39 ILE A 42 5 4 HELIX 2 2 ASP A 80 ILE A 83 5 4 HELIX 3 3 ASP A 127 ILE A 130 5 4 SHEET 1 A 4 VAL A 12 SER A 16 0 SHEET 2 A 4 TRP A 132 PRO A 136 -1 O SER A 135 N LEU A 13 SHEET 3 A 4 GLU A 94 SER A 99 -1 N VAL A 95 O TRP A 132 SHEET 4 A 4 TRP A 85 GLY A 91 -1 N GLU A 90 O GLU A 94 SHEET 1 B 2 TRP A 22 ILE A 25 0 SHEET 2 B 2 VAL A 31 THR A 34 -1 O ASP A 32 N ARG A 24 SHEET 1 C 2 TRP A 44 GLY A 50 0 SHEET 2 C 2 GLU A 53 SER A 58 -1 O ARG A 57 N GLN A 45 SHEET 1 D 2 TRP A 64 ILE A 67 0 SHEET 2 D 2 VAL A 73 THR A 76 -1 O THR A 76 N TRP A 64 SHEET 1 E 2 TRP A 108 ILE A 111 0 SHEET 2 E 2 VAL A 117 THR A 123 -1 O ASP A 118 N ARG A 110 SITE 1 AC1 9 THR A 30 VAL A 31 THR A 72 VAL A 73 SITE 2 AC1 9 THR A 116 VAL A 117 HOH A 310 HOH A 326 SITE 3 AC1 9 HOH A 327 SITE 1 AC2 8 ARG A 76A GLN A 107 GLY A 119 THR A 123 SITE 2 AC2 8 ARG A 123A HOH A 346 HOH A 367 HOH A 421 CRYST1 47.138 48.471 69.691 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 0.021214 0.000000 0.000000 0.00000 SCALE2 0.000000 0.020631 0.000000 0.00000 SCALE3 0.000000 0.000000 0.014349 0.00000