PDB Short entry for 3V1A HEADER DE NOVO PROTEIN, METAL BINDING PROTEIN 09-DEC-11 3V1A TITLE CRYSTAL STRUCTURE OF DE NOVO DESIGNED MID1-APO1 COMPND MOL_ID: 1; COMPND 2 MOLECULE: COMPUTATIONAL DESIGN, MID1-APO1; COMPND 3 CHAIN: A; 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, DE NOVO PROTEIN, METAL KEYWDS 2 BINDING PROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR B.S.DER,M.MACHIUS,M.J.MILEY,B.KUHLMAN REVDAT 3 13-SEP-23 3V1A 1 REMARK REVDAT 2 07-MAR-12 3V1A 1 JRNL REVDAT 1 11-JAN-12 3V1A 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. 0.98 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) : 0.98 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 18.18 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.340 REMARK 3 COMPLETENESS FOR RANGE (%) : 96.7 REMARK 3 NUMBER OF REFLECTIONS : 20588 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.095 REMARK 3 R VALUE (WORKING SET) : 0.094 REMARK 3 FREE R VALUE : 0.113 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.130 REMARK 3 FREE R VALUE TEST SET COUNT : 1057 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 18.1809 - 1.9580 0.97 2605 134 0.1204 0.1326 REMARK 3 2 1.9580 - 1.5544 1.00 2557 131 0.0854 0.1076 REMARK 3 3 1.5544 - 1.3580 0.99 2461 163 0.0774 0.0985 REMARK 3 4 1.3580 - 1.2339 0.98 2457 128 0.0728 0.1009 REMARK 3 5 1.2339 - 1.1454 0.98 2421 151 0.0712 0.0982 REMARK 3 6 1.1454 - 1.0779 0.96 2426 124 0.0727 0.0985 REMARK 3 7 1.0779 - 1.0239 0.97 2405 131 0.0851 0.1133 REMARK 3 8 1.0239 - 0.9794 0.88 2199 95 0.1102 0.1359 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : FLAT BULK SOLVENT MODEL REMARK 3 SOLVENT RADIUS : 1.00 REMARK 3 SHRINKAGE RADIUS : 0.73 REMARK 3 K_SOL : 0.47 REMARK 3 B_SOL : 55.10 REMARK 3 REMARK 3 ERROR ESTIMATES. REMARK 3 COORDINATE ERROR (MAXIMUM-LIKELIHOOD BASED) : 0.060 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 8.390 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 7.30 REMARK 3 MEAN B VALUE (OVERALL, A**2) : NULL REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -1.71810 REMARK 3 B22 (A**2) : -1.06140 REMARK 3 B33 (A**2) : 2.77950 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 : 0.017 486 REMARK 3 ANGLE : 1.640 667 REMARK 3 CHIRALITY : 0.091 67 REMARK 3 PLANARITY : 0.011 97 REMARK 3 DIHEDRAL : 16.948 196 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 3V1A 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_1000069468. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 11-NOV-10 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 5.97 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) : 0.9794 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 : 20751 REMARK 200 RESOLUTION RANGE HIGH (A) : 0.980 REMARK 200 RESOLUTION RANGE LOW (A) : 18.180 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : -3.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 97.2 REMARK 200 DATA REDUNDANCY : 10.00 REMARK 200 R MERGE (I) : 0.09100 REMARK 200 R SYM (I) : NULL REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 11.1000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 0.98 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 0.99 REMARK 200 COMPLETENESS FOR SHELL (%) : 77.6 REMARK 200 DATA REDUNDANCY IN SHELL : 3.60 REMARK 200 R MERGE FOR SHELL (I) : 0.21400 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 <I/SIGMA(I)> FOR SHELL : 5.400 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: PDB ENTRY 1YZM REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 24.45 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 1.63 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.1 MICROLITERS PROTEIN (20 MG/ML, 100 REMARK 280 MM AMMONIUM ACETATE BUFFER) MIXED WITH 0.1-0.2 MICROLITERS REMARK 280 CRYSTALLIZATION BUFFER (0.1 M MES PH 5.97, 30% PEG 600, 7.5% PEG REMARK 280 1000, 5% GLYCEROL), VAPOR DIFFUSION, SITTING DROP, TEMPERATURE REMARK 280 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 12.63200 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 21.45800 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 16.51450 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 21.45800 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 12.63200 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 16.51450 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 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: 3V1B RELATED DB: PDB REMARK 900 RELATED ID: 3V1C 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 3V1A A -1 46 PDB 3V1A 3V1A -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 FORMUL 2 HOH *52(H2 O) HELIX 1 1 SER A 2 ALA A 20 1 19 HELIX 2 2 ARG A 23 GLN A 44 1 22 CRYST1 25.264 33.029 42.916 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 0.039582 0.000000 0.000000 0.00000 SCALE2 0.000000 0.030276 0.000000 0.00000 SCALE3 0.000000 0.000000 0.023301 0.00000