HEADER PHOTOSYNTHESIS 17-OCT-24 9H41 TITLE APO-HELICAL CAROTENOID PROTEIN 4 (HCP4) FROM ANABAENA G152C MUTANT COMPND MOL_ID: 1; COMPND 2 MOLECULE: ORANGE CAROTENOID-BINDING DOMAIN-CONTAINING PROTEIN; COMPND 3 CHAIN: A; COMPND 4 ENGINEERED: YES; COMPND 5 MUTATION: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: NOSTOC SP. (STRAIN PCC 7120 / SAG 25.82 / UTEX SOURCE 3 2576); SOURCE 4 ORGANISM_TAXID: 103690; SOURCE 5 GENE: ALL4941; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21(DE3); SOURCE 7 EXPRESSION_SYSTEM_TAXID: 469008 KEYWDS NON PHOTOCHEMICAL QUENCHING ORANGE CAROTENOID BINDING PROTEIN KEYWDS 2 CYANOBACTERIA PHYCOBILISOME PHOTOPROTECTION, PHOTOSYNTHESIS EXPDTA X-RAY DIFFRACTION AUTHOR J.SKLYAR,N.ADIR REVDAT 1 11-JUN-25 9H41 0 JRNL AUTH J.SKLYAR,F.GLASER,N.ADIR JRNL TITL THE APO-HCP4 STRUCTURE REVEALS FACETS OF CAROTENOID UPTAKE. JRNL REF INT.J.BIOL.MACROMOL. V. 315 44290 2025 JRNL REFN ISSN 0141-8130 JRNL PMID 40398757 JRNL DOI 10.1016/J.IJBIOMAC.2025.144290 REMARK 2 REMARK 2 RESOLUTION. 3.09 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX (1.20.1_4487: ???) 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) : 3.09 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 9.97 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.340 REMARK 3 COMPLETENESS FOR RANGE (%) : 98.1 REMARK 3 NUMBER OF REFLECTIONS : 7010 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.204 REMARK 3 R VALUE (WORKING SET) : 0.202 REMARK 3 FREE R VALUE : 0.243 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.950 REMARK 3 FREE R VALUE TEST SET COUNT : 347 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 9.9700 - 3.8600 1.00 3406 168 0.1837 0.2292 REMARK 3 2 3.8600 - 3.0900 0.96 3257 179 0.2308 0.2624 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) : 0.260 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 23.620 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : NULL 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 : 0.010 NULL REMARK 3 ANGLE : 1.161 NULL REMARK 3 CHIRALITY : 0.074 188 REMARK 3 PLANARITY : 0.007 203 REMARK 3 DIHEDRAL : 6.163 158 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 9H41 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 17-OCT-24. REMARK 100 THE DEPOSITION ID IS D_1292142491. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 15-SEP-24 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 8.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : ESRF REMARK 200 BEAMLINE : MASSIF-1 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.9655 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS PILATUS 6M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : POINTLESS REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 40807 REMARK 200 RESOLUTION RANGE HIGH (A) : 3.090 REMARK 200 RESOLUTION RANGE LOW (A) : 9.970 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 96.1 REMARK 200 DATA REDUNDANCY : 10.10 REMARK 200 R MERGE (I) : 0.14000 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 11.9000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 3.09 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 3.34 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: PHASER REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 56.35 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.70 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.08M TRIS PH 8.5, 1.6M AMMONIUM REMARK 280 DIHYDROGEN PHOSPHATE, 20% V/V GLYCEROL, VAPOR DIFFUSION, HANGING REMARK 280 DROP, TEMPERATURE 293K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 43 21 2 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 -Y+1/2,X+1/2,Z+3/4 REMARK 290 4555 Y+1/2,-X+1/2,Z+1/4 REMARK 290 5555 -X+1/2,Y+1/2,-Z+3/4 REMARK 290 6555 X+1/2,-Y+1/2,-Z+1/4 REMARK 290 7555 Y,X,-Z REMARK 290 8555 -Y,-X,-Z+1/2 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 56.19450 REMARK 290 SMTRY1 3 0.000000 -1.000000 0.000000 30.43550 REMARK 290 SMTRY2 3 1.000000 0.000000 0.000000 30.43550 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 84.29175 REMARK 290 SMTRY1 4 0.000000 1.000000 0.000000 30.43550 REMARK 290 SMTRY2 4 -1.000000 0.000000 0.000000 30.43550 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 28.09725 REMARK 290 SMTRY1 5 -1.000000 0.000000 0.000000 30.43550 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 30.43550 REMARK 290 SMTRY3 5 0.000000 0.000000 -1.000000 84.29175 REMARK 290 SMTRY1 6 1.000000 0.000000 0.000000 30.43550 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 30.43550 REMARK 290 SMTRY3 6 0.000000 0.000000 -1.000000 28.09725 REMARK 290 SMTRY1 7 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY2 7 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 8 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY2 8 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 8 0.000000 0.000000 -1.000000 56.19450 REMARK 290 REMARK 290 REMARK: NULL REMARK 300 REMARK 300 BIOMOLECULE: 1, 2 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: 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 350 REMARK 350 BIOMOLECULE: 2 REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 840 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 15440 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -12.0 KCAL/MOL 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 350 BIOMT1 2 0.000000 -1.000000 0.000000 0.00000 REMARK 350 BIOMT2 2 -1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT3 2 0.000000 0.000000 -1.000000 56.19450 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 THR A 3 REMARK 465 PHE A 4 REMARK 465 THR A 5 REMARK 465 SER A 6 REMARK 465 ASP A 7 REMARK 465 SER A 8 REMARK 465 ALA A 9 REMARK 465 SER A 10 REMARK 465 THR A 11 REMARK 465 ARG A 12 REMARK 465 ALA A 59 REMARK 465 THR A 60 REMARK 465 GLY A 61 REMARK 465 ALA A 62 REMARK 465 ALA A 63 REMARK 465 ARG A 64 REMARK 465 LEU A 65 REMARK 465 GLN A 66 REMARK 465 LEU A 67 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 THR A 49 NH1 ARG A 100 6545 2.14 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 ALA A 16 49.84 -108.52 REMARK 500 ILE A 19 -152.53 -88.06 REMARK 500 ALA A 24 -53.58 62.90 REMARK 500 PRO A 57 154.22 -42.90 REMARK 500 VAL A 129 156.52 65.21 REMARK 500 REMARK 500 REMARK: NULL DBREF 9H41 A 3 171 UNP Q8YMJ2 CROTO_NOSS1 2 170 SEQADV 9H41 CYS A 152 UNP Q8YMJ2 GLY 151 ENGINEERED MUTATION SEQRES 1 A 169 THR PHE THR SER ASP SER ALA SER THR ARG PHE SER GLN SEQRES 2 A 169 ALA PHE GLY ILE GLN THR GLY ASP ALA VAL ALA SER THR SEQRES 3 A 169 ILE THR VAL PHE GLN ALA LEU SER ILE ASP ASP GLN LEU SEQRES 4 A 169 ALA VAL LEU TRP TYR ALA TYR THR GLU MET GLY ARG SER SEQRES 5 A 169 ILE THR PRO ALA ALA THR GLY ALA ALA ARG LEU GLN LEU SEQRES 6 A 169 ALA GLU GLY LEU LEU ASN GLN ILE LYS GLN MET SER HIS SEQRES 7 A 169 ALA GLU GLN LEU GLN VAL MET ARG ASP LEU ALA ALA LYS SEQRES 8 A 169 ASN ASN THR GLN VAL SER ARG SER TYR GLY ILE LEU SER SEQRES 9 A 169 ASN ASN THR LYS LEU ALA PHE TRP TYR GLU LEU SER GLU SEQRES 10 A 169 LEU MET VAL LYS GLY PHE VAL VAL PRO VAL PRO THR ASP SEQRES 11 A 169 TYR LYS ILE SER ARG ASP GLY SER GLN VAL LEU GLU ALA SEQRES 12 A 169 LEU LYS GLY LEU ASP PHE CYS GLN GLN ILE THR VAL LEU SEQRES 13 A 169 ARG LYS VAL VAL ALA ASP MET GLY VAL ASP PRO LEU ALA HELIX 1 AA1 ALA A 24 ALA A 34 1 11 HELIX 2 AA2 SER A 36 GLY A 52 1 17 HELIX 3 AA3 GLU A 69 GLN A 77 1 9 HELIX 4 AA4 SER A 79 ALA A 92 1 14 HELIX 5 AA5 THR A 96 ILE A 104 1 9 HELIX 6 AA6 SER A 106 LYS A 123 1 18 HELIX 7 AA7 SER A 136 GLY A 148 1 13 HELIX 8 AA8 ASP A 150 ASP A 164 1 15 SSBOND 1 CYS A 152 CYS A 152 1555 8555 2.05 CRYST1 60.871 60.871 112.389 90.00 90.00 90.00 P 43 21 2 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 0.016428 0.000000 0.000000 0.00000 SCALE2 0.000000 0.016428 0.000000 0.00000 SCALE3 0.000000 0.000000 0.008898 0.00000 TER 1161 ALA A 171 MASTER 286 0 0 8 0 0 0 6 1160 1 0 13 END