HEADER DE NOVO PROTEIN 12-JUL-24 9G3B TITLE CRYSTAL STRUCTURE OF THE ARTIFICIAL PROTEIN METP IN COMPLEX WITH TITLE 2 CADMIUM ION AT DIFFERENT TEMPERATURE, 130 K COMPND MOL_ID: 1; COMPND 2 MOLECULE: METP ARTIFICIAL PROTEIN; COMPND 3 CHAIN: C; COMPND 4 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 SYNTHETIC: YES; SOURCE 3 ORGANISM_SCIENTIFIC: SYNTHETIC CONSTRUCT; SOURCE 4 ORGANISM_TAXID: 32630 KEYWDS DE NOVO DESIGN, ROOM TEMPERATURE, CADMIUM-SULPHUR CLUSTER, DENOVO KEYWDS 2 PROTEIN, DE NOVO PROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR L.DI COSTANZO,S.LA GATTA,M.CHINO REVDAT 2 22-JAN-25 9G3B 1 JRNL REVDAT 1 04-DEC-24 9G3B 0 JRNL AUTH L.F.DI COSTANZO,G.SGUEGLIA,C.ORLANDO,M.POLENTARUTTI,L.LEONE, JRNL AUTH 2 S.LA GATTA,M.DE FENZA,L.DE GIOIA,A.LOMBARDI,F.ARRIGONI, JRNL AUTH 3 M.CHINO JRNL TITL STRUCTURAL INSIGHTS INTO TEMPERATURE-DEPENDENT DYNAMICS OF JRNL TITL 2 METPSC1, A MINIATURIZED ELECTRON-TRANSFER PROTEIN. JRNL REF J.INORG.BIOCHEM. V. 264 12810 2025 JRNL REFN ISSN 0162-0134 JRNL PMID 39689412 JRNL DOI 10.1016/J.JINORGBIO.2024.112810 REMARK 2 REMARK 2 RESOLUTION. 1.90 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.21_5207 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 : GEOSTD + MONOMER LIBRARY + CDL V1.2 REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.90 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 29.37 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.340 REMARK 3 COMPLETENESS FOR RANGE (%) : 98.1 REMARK 3 NUMBER OF REFLECTIONS : 1585 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.149 REMARK 3 R VALUE (WORKING SET) : 0.144 REMARK 3 FREE R VALUE : NULL REMARK 3 FREE R VALUE TEST SET SIZE (%) : NULL REMARK 3 FREE R VALUE TEST SET COUNT : NULL 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 29.3700 - 1.9000 0.98 1513 0 0.1435 0.0000 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 : 0.90 REMARK 3 K_SOL : NULL REMARK 3 B_SOL : NULL REMARK 3 REMARK 3 ERROR ESTIMATES. REMARK 3 COORDINATE ERROR (MAXIMUM-LIKELIHOOD BASED) : 0.259 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 9.890 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 15.15 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 20.31 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 : 0.013 204 REMARK 3 ANGLE : 1.335 276 REMARK 3 CHIRALITY : 0.085 25 REMARK 3 PLANARITY : 0.014 38 REMARK 3 DIHEDRAL : 17.329 74 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 9G3B COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 12-JUL-24. REMARK 100 THE DEPOSITION ID IS D_1292140202. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 01-JAN-00 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 7.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : ELETTRA REMARK 200 BEAMLINE : 5.2R REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.534 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS PILATUS3 6M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : SCALA REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 8740 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.700 REMARK 200 RESOLUTION RANGE LOW (A) : 29.370 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 95.1 REMARK 200 DATA REDUNDANCY : 2.200 REMARK 200 R MERGE (I) : 0.07900 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 8.8200 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.70 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.80 REMARK 200 COMPLETENESS FOR SHELL (%) : 96.3 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: SAD REMARK 200 SOFTWARE USED: PHASER REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 56.60 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.80 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: DROP CONTAINING 2.0 μL OF 1:1 REMARK 280 (V/V) MIXTURE OF PROTEIN SOLUTION (10 MG/ML, 7 MM DTT, 4 MM REMARK 280 CDCL2) AND 2.0 μL OF PRECIPITANT BUFFER (0.1 M HEPES AT PH REMARK 280 7.5, 1.4 M SODIUM CITRATE TRIBASIC DIHYDRATE) WAS EQUILIBRATED REMARK 280 AGAINST 0.5 ML RESERVOIR OF PRECIPITANT BUFFER, VAPOR DIFFUSION, REMARK 280 HANGING DROP, TEMPERATURE 298K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: C 2 2 21 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,-Y,Z+1/2 REMARK 290 3555 -X,Y,-Z+1/2 REMARK 290 4555 X,-Y,-Z REMARK 290 5555 X+1/2,Y+1/2,Z REMARK 290 6555 -X+1/2,-Y+1/2,Z+1/2 REMARK 290 7555 -X+1/2,Y+1/2,-Z+1/2 REMARK 290 8555 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 0.00000 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 9.57400 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 9.57400 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 4 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 5 1.000000 0.000000 0.000000 17.20950 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 28.17600 REMARK 290 SMTRY3 5 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 6 -1.000000 0.000000 0.000000 17.20950 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 28.17600 REMARK 290 SMTRY3 6 0.000000 0.000000 1.000000 9.57400 REMARK 290 SMTRY1 7 -1.000000 0.000000 0.000000 17.20950 REMARK 290 SMTRY2 7 0.000000 1.000000 0.000000 28.17600 REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 9.57400 REMARK 290 SMTRY1 8 1.000000 0.000000 0.000000 17.20950 REMARK 290 SMTRY2 8 0.000000 -1.000000 0.000000 28.17600 REMARK 290 SMTRY3 8 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 APPLY THE FOLLOWING TO CHAINS: C 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 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 O HOH C 204 O HOH C 211 3556 1.74 REMARK 500 O HOH C 203 O HOH C 208 8556 1.94 REMARK 500 O HOH C 218 O HOH C 218 4556 2.13 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 CD C 101 CD REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS C 2 SG REMARK 620 2 CYS C 5 SG 111.1 REMARK 620 3 CYS C 17 SG 111.7 107.0 REMARK 620 4 CYS C 20 SG 106.6 110.4 110.2 REMARK 620 N 1 2 3 DBREF 9G3B C 0 29 PDB 9G3B 9G3B 0 29 SEQRES 1 C 30 ACE TYR CYS SER ASP CYS GLY ALA ASP AIB SER GLN VAL SEQRES 2 C 30 ARG GLY GLY TYR CYS THR ASN CYS GLY ALA SER AIB ASP SEQRES 3 C 30 ARG ILE ARG NH2 HET ACE C 0 6 HET AIB C 9 13 HET AIB C 24 13 HET NH2 C 29 3 HET CD C 101 1 HETNAM ACE ACETYL GROUP HETNAM AIB ALPHA-AMINOISOBUTYRIC ACID HETNAM NH2 AMINO GROUP HETNAM CD CADMIUM ION FORMUL 1 ACE C2 H4 O FORMUL 1 AIB 2(C4 H9 N O2) FORMUL 1 NH2 H2 N FORMUL 2 CD CD 2+ FORMUL 3 HOH *18(H2 O) HELIX 1 AA1 ASP C 8 SER C 10 5 3 HELIX 2 AA2 SER C 23 ASP C 25 5 3 SHEET 1 AA1 2 TYR C 1 CYS C 2 0 SHEET 2 AA1 2 ILE C 27 ARG C 28 -1 O ARG C 28 N TYR C 1 SHEET 1 AA2 2 VAL C 12 ARG C 13 0 SHEET 2 AA2 2 TYR C 16 CYS C 17 -1 O TYR C 16 N ARG C 13 LINK C ACE C 0 N TYR C 1 1555 1555 1.34 LINK C ASP C 8 N AIB C 9 1555 1555 1.32 LINK C AIB C 9 N SER C 10 1555 1555 1.33 LINK C SER C 23 N AIB C 24 1555 1555 1.33 LINK C AIB C 24 N ASP C 25 1555 1555 1.32 LINK C ARG C 28 N NH2 C 29 1555 1555 1.43 LINK SG CYS C 2 CD CD C 101 1555 1555 2.46 LINK SG CYS C 5 CD CD C 101 1555 1555 2.56 LINK SG CYS C 17 CD CD C 101 1555 1555 2.57 LINK SG CYS C 20 CD CD C 101 1555 1555 2.53 CRYST1 34.419 56.352 19.148 90.00 90.00 90.00 C 2 2 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 0.029054 0.000000 0.000000 0.00000 SCALE2 0.000000 0.017746 0.000000 0.00000 SCALE3 0.000000 0.000000 0.052225 0.00000 CONECT 1 2 3 7 CONECT 2 1 CONECT 3 1 4 5 6 CONECT 4 3 CONECT 5 3 CONECT 6 3 CONECT 7 1 CONECT 33 388 CONECT 66 388 CONECT 90 100 CONECT 100 90 101 106 CONECT 101 100 102 104 105 CONECT 102 101 103 113 CONECT 103 102 CONECT 104 101 107 108 109 CONECT 105 101 110 111 112 CONECT 106 100 CONECT 107 104 CONECT 108 104 CONECT 109 104 CONECT 110 105 CONECT 111 105 CONECT 112 105 CONECT 113 102 CONECT 221 388 CONECT 259 388 CONECT 283 292 CONECT 292 283 293 298 CONECT 293 292 294 296 297 CONECT 294 293 295 305 CONECT 295 294 CONECT 296 293 299 300 301 CONECT 297 293 302 303 304 CONECT 298 292 CONECT 299 296 CONECT 300 296 CONECT 301 296 CONECT 302 297 CONECT 303 297 CONECT 304 297 CONECT 305 294 CONECT 362 384 CONECT 384 362 385 386 CONECT 385 384 CONECT 386 384 CONECT 388 33 66 221 259 MASTER 241 0 5 2 4 0 0 6 223 1 46 3 END