HEADER DE NOVO PROTEIN, HYDROLASE 09-DEC-11 3V1C TITLE CRYSTAL STRUCTURE OF DE NOVO DESIGNED MID1-ZINC COMPND MOL_ID: 1; COMPND 2 MOLECULE: COMPUTATIONAL DESIGN, MID1-ZINC; COMPND 3 CHAIN: A, B; COMPND 4 SYNONYM: COMPUTATIONAL REDESIGN OF THE BIOLOGICAL SEQUENCE.; COMPND 5 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: ARTIFICIAL GENE; SOURCE 3 ORGANISM_TAXID: 32630; SOURCE 4 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 5 EXPRESSION_SYSTEM_TAXID: 511693; SOURCE 6 EXPRESSION_SYSTEM_STRAIN: BL21; SOURCE 7 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 8 EXPRESSION_SYSTEM_PLASMID: PQE-80L MBP FUSION KEYWDS HELIX-TURN-HELIX, METAL BINDING, HOMODIMER, METAL BINDING PROTEIN, KEYWDS 2 HYDROLASE, DE NOVO PROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR B.S.DER,M.MACHIUS,M.J.MILEY,B.KUHLMAN REVDAT 3 13-SEP-23 3V1C 1 REMARK LINK REVDAT 2 07-MAR-12 3V1C 1 JRNL REVDAT 1 11-JAN-12 3V1C 0 JRNL AUTH B.S.DER,M.MACHIUS,M.J.MILEY,J.L.MILLS,T.SZYPERSKI,B.KUHLMAN JRNL TITL METAL-MEDIATED AFFINITY AND ORIENTATION SPECIFICITY IN A JRNL TITL 2 COMPUTATIONALLY DESIGNED PROTEIN HOMODIMER. JRNL REF J.AM.CHEM.SOC. V. 134 375 2012 JRNL REFN ISSN 0002-7863 JRNL PMID 22092237 JRNL DOI 10.1021/JA208015J REMARK 2 REMARK 2 RESOLUTION. 1.13 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX (PHENIX.REFINE: 1.7.3_927) 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) : 1.13 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 19.29 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.340 REMARK 3 COMPLETENESS FOR RANGE (%) : 97.8 REMARK 3 NUMBER OF REFLECTIONS : 30257 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.148 REMARK 3 R VALUE (WORKING SET) : 0.147 REMARK 3 FREE R VALUE : 0.176 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.030 REMARK 3 FREE R VALUE TEST SET COUNT : 1523 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 19.2948 - 2.5088 0.94 2673 157 0.1692 0.1908 REMARK 3 2 2.5088 - 1.9920 0.97 2648 137 0.1388 0.1708 REMARK 3 3 1.9920 - 1.7403 0.98 2635 150 0.1331 0.1661 REMARK 3 4 1.7403 - 1.5813 0.99 2612 133 0.1242 0.1685 REMARK 3 5 1.5813 - 1.4680 0.99 2659 140 0.1227 0.1633 REMARK 3 6 1.4680 - 1.3815 1.00 2650 140 0.1244 0.1527 REMARK 3 7 1.3815 - 1.3123 1.00 2621 131 0.1238 0.1575 REMARK 3 8 1.3123 - 1.2552 1.00 2612 159 0.1295 0.1618 REMARK 3 9 1.2552 - 1.2069 1.00 2606 137 0.1454 0.1726 REMARK 3 10 1.2069 - 1.1652 0.99 2630 128 0.1774 0.2033 REMARK 3 11 1.1652 - 1.1288 0.91 2388 111 0.2077 0.2291 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : FLAT BULK SOLVENT MODEL REMARK 3 SOLVENT RADIUS : 0.90 REMARK 3 SHRINKAGE RADIUS : 0.60 REMARK 3 K_SOL : 0.41 REMARK 3 B_SOL : 43.90 REMARK 3 REMARK 3 ERROR ESTIMATES. REMARK 3 COORDINATE ERROR (MAXIMUM-LIKELIHOOD BASED) : 0.100 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 13.960 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 9.02 REMARK 3 MEAN B VALUE (OVERALL, A**2) : NULL REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -1.26800 REMARK 3 B22 (A**2) : 0.70550 REMARK 3 B33 (A**2) : 0.56240 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 : 0.013 897 REMARK 3 ANGLE : 1.241 1228 REMARK 3 CHIRALITY : 0.072 126 REMARK 3 PLANARITY : 0.006 172 REMARK 3 DIHEDRAL : 14.840 360 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 3V1C COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 12-DEC-11. REMARK 100 THE DEPOSITION ID IS D_1000069470. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 26-APR-11 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 5.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : APS REMARK 200 BEAMLINE : 23-ID-B REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.9180 REMARK 200 MONOCHROMATOR : DOUBLE CRYSTAL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : MARMOSAIC 300 MM CCD REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : HKL-2000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 30296 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.129 REMARK 200 RESOLUTION RANGE LOW (A) : 19.292 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : -3.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 97.8 REMARK 200 DATA REDUNDANCY : 7.300 REMARK 200 R MERGE (I) : 0.08900 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 31.4000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.13 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.14 REMARK 200 COMPLETENESS FOR SHELL (%) : 88.8 REMARK 200 DATA REDUNDANCY IN SHELL : 2.50 REMARK 200 R MERGE FOR SHELL (I) : 0.49000 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 2.000 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: PHASER REMARK 200 SOFTWARE USED: PHASER REMARK 200 STARTING MODEL: PDB ENTRY 1YZM REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 31.95 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 1.81 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 1-2 MICROLITER2 PROTEIN (20 MG/ML, 100 REMARK 280 MM AMMONIUM ACETATE BUFFER) MIXED WITH 1 MICROLITER REMARK 280 CRYSTALLIZATION BUFFER (0.1 M SODIUM CITRATE, PH 5.5, 1.25 M REMARK 280 AMMONIUM SULFATE, 0.08 M K/NA TARTRATE), VAPOR DIFFUSION, REMARK 280 HANGING DROP, TEMPERATURE 293K 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 12.65600 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 52.70600 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 14.90000 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 52.70600 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 12.65600 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 14.90000 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 300 REMARK: IN THE CRYSTAL STRUCTURE, THE BIOLOGICAL ASSEMBLY (DIMER) REMARK 300 IS LOCATED WITHIN THE ASYMMETRIC UNIT. 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 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 1870 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 6560 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -76.0 KCAL/MOL 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 GLY A -1 REMARK 465 SER A 0 REMARK 465 GLY B -1 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 SD MET A 38 O HOH A 253 2.17 REMARK 500 REMARK 500 REMARK: NULL REMARK 620 REMARK 620 METAL COORDINATION REMARK 620 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 620 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE): REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 ZN A 101 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HIS A 12 NE2 REMARK 620 2 HIS A 16 NE2 100.6 REMARK 620 3 TLA A 102 O41 96.7 115.9 REMARK 620 4 HIS B 39 ND1 115.7 107.8 118.6 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 ZN B 101 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HIS A 39 ND1 REMARK 620 2 HIS B 12 NE2 106.5 REMARK 620 3 HIS B 16 NE2 108.1 103.0 REMARK 620 N 1 2 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ZN A 101 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE TLA A 102 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ZN B 101 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 1YZM RELATED DB: PDB REMARK 900 THIS DEPOSITION IS A COMPUTATIONAL REDESIGN OF 1YZM. REMARK 900 RELATED ID: 3V1A RELATED DB: PDB REMARK 900 RELATED ID: 3V1B RELATED DB: PDB REMARK 900 RELATED ID: 3V1D RELATED DB: PDB REMARK 900 RELATED ID: 3V1E RELATED DB: PDB REMARK 900 RELATED ID: 3V1F RELATED DB: PDB DBREF 3V1C A -1 46 PDB 3V1C 3V1C -1 46 DBREF 3V1C B -1 46 PDB 3V1C 3V1C -1 46 SEQRES 1 A 48 GLY SER GLY SER PRO LEU ALA GLN GLN ILE LYS ASN ILE SEQRES 2 A 48 HIS SER PHE ILE HIS GLN ALA LYS ALA ALA GLY ARG MET SEQRES 3 A 48 ASP GLU VAL ARG THR LEU GLN GLU ASN LEU HIS GLN LEU SEQRES 4 A 48 MET HIS GLU TYR PHE GLN GLN SER ASP SEQRES 1 B 48 GLY SER GLY SER PRO LEU ALA GLN GLN ILE LYS ASN ILE SEQRES 2 B 48 HIS SER PHE ILE HIS GLN ALA LYS ALA ALA GLY ARG MET SEQRES 3 B 48 ASP GLU VAL ARG THR LEU GLN GLU ASN LEU HIS GLN LEU SEQRES 4 B 48 MET HIS GLU TYR PHE GLN GLN SER ASP HET ZN A 101 1 HET TLA A 102 14 HET UNL A 103 13 HET ZN B 101 1 HETNAM ZN ZINC ION HETNAM TLA L(+)-TARTARIC ACID HETNAM UNL UNKNOWN LIGAND FORMUL 3 ZN 2(ZN 2+) FORMUL 4 TLA C4 H6 O6 FORMUL 7 HOH *100(H2 O) HELIX 1 1 SER A 2 ALA A 21 1 20 HELIX 2 2 ARG A 23 GLN A 43 1 21 HELIX 3 3 SER B 2 ALA B 20 1 19 HELIX 4 4 ARG B 23 PHE B 42 1 20 LINK NE2 HIS A 12 ZN ZN A 101 1555 1555 2.03 LINK NE2 HIS A 16 ZN ZN A 101 1555 1555 2.01 LINK ND1 HIS A 39 ZN ZN B 101 1555 1555 2.04 LINK ZN ZN A 101 O41 TLA A 102 1555 1555 1.95 LINK ZN ZN A 101 ND1 HIS B 39 1555 1555 2.00 LINK NE2 HIS B 12 ZN ZN B 101 1555 1555 2.02 LINK NE2 HIS B 16 ZN ZN B 101 1555 1555 2.01 SITE 1 AC1 4 HIS A 12 HIS A 16 TLA A 102 HIS B 39 SITE 1 AC2 11 HIS A 12 HIS A 16 LYS A 19 ARG A 23 SITE 2 AC2 11 GLN A 31 HIS A 35 ZN A 101 HOH A 228 SITE 3 AC2 11 HOH A 237 HIS B 35 HIS B 39 SITE 1 AC3 4 HIS A 39 HIS B 12 HIS B 16 ASP B 46 CRYST1 25.312 29.800 105.412 90.00 90.00 90.00 P 21 21 21 8 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 0.039507 0.000000 0.000000 0.00000 SCALE2 0.000000 0.033557 0.000000 0.00000 SCALE3 0.000000 0.000000 0.009487 0.00000