HEADER STRUCTURAL PROTEIN 31-MAY-21 7N3A TITLE CRYSTAL STRUCTURE OF 9-SITE DEAMIDATED VARIANT OF HUMAN GAMMA(S)- TITLE 2 CRYSTALLIN COMPND MOL_ID: 1; COMPND 2 MOLECULE: GAMMA-CRYSTALLIN S; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: BETA-CRYSTALLIN S,GAMMA-S-CRYSTALLIN; COMPND 5 ENGINEERED: YES; COMPND 6 MUTATION: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 3 ORGANISM_COMMON: HUMAN; SOURCE 4 ORGANISM_TAXID: 9606; SOURCE 5 GENE: CRYGS, CRYG8; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS STRUCTURAL PROTEIN, CRYSTALLIN, HUMAN CRYSTALLIN, GAMMA(S) KEYWDS 2 CRYSTALLIN, EYE LENS PROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR B.NORTON-BAKER,P.MEHRABI,R.W.MARTIN REVDAT 3 18-OCT-23 7N3A 1 REMARK REVDAT 2 05-OCT-22 7N3A 1 JRNL REVDAT 1 23-MAR-22 7N3A 0 JRNL AUTH B.NORTON-BAKER,P.MEHRABI,A.O.KWOK,K.W.ROSKAMP,M.A.ROCHA, JRNL AUTH 2 M.A.SPRAGUE-PIERCY,D.VON STETTEN,R.J.D.MILLER,R.W.MARTIN JRNL TITL DEAMIDATION OF THE HUMAN EYE LENS PROTEIN GAMMA S-CRYSTALLIN JRNL TITL 2 ACCELERATES OXIDATIVE AGING. JRNL REF STRUCTURE V. 30 763 2022 JRNL REFN ISSN 0969-2126 JRNL PMID 35338852 JRNL DOI 10.1016/J.STR.2022.03.002 REMARK 2 REMARK 2 RESOLUTION. 1.50 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.18.2_3874 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) : 1.50 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 43.74 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.340 REMARK 3 COMPLETENESS FOR RANGE (%) : 98.4 REMARK 3 NUMBER OF REFLECTIONS : 23378 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 : 0.224 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.910 REMARK 3 FREE R VALUE TEST SET COUNT : 1147 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 43.7400 - 3.0000 0.99 2852 142 0.1471 0.1640 REMARK 3 2 3.0000 - 2.3800 0.99 2817 152 0.2040 0.2390 REMARK 3 3 2.3800 - 2.0800 0.98 2747 168 0.2054 0.2295 REMARK 3 4 2.0800 - 1.8900 0.99 2782 152 0.2230 0.2794 REMARK 3 5 1.8900 - 1.7500 0.99 2780 133 0.2677 0.3118 REMARK 3 6 1.7500 - 1.6500 0.98 2776 121 0.3200 0.3373 REMARK 3 7 1.6500 - 1.5700 0.98 2749 143 0.3819 0.4605 REMARK 3 8 1.5700 - 1.5000 0.97 2728 136 0.4508 0.4857 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : FLAT BULK SOLVENT MODEL REMARK 3 SOLVENT RADIUS : 1.11 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) : 0.223 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 37.705 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 25.38 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 36.02 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 : 0.008 1517 REMARK 3 ANGLE : 0.987 2058 REMARK 3 CHIRALITY : 0.070 198 REMARK 3 PLANARITY : 0.007 271 REMARK 3 DIHEDRAL : 23.827 565 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 7N3A COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 01-JUN-21. REMARK 100 THE DEPOSITION ID IS D_1000257284. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 25-AUG-20 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : NULL REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : PETRA III, EMBL C/O DESY REMARK 200 BEAMLINE : P14 (MX2) REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.9762 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS EIGER X 16M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : XSCALE REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 23517 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.500 REMARK 200 RESOLUTION RANGE LOW (A) : 43.740 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 98.4 REMARK 200 DATA REDUNDANCY : 6.800 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 13.8500 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.50 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.55 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: 6FD8 REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 31.36 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 1.79 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.1 M SODIUM ACETATE PH 5.45, 21% PEG REMARK 280 3350, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 293K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 1 21 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,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 28.85500 REMARK 290 SMTRY3 2 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 GLY A 1 REMARK 465 SER A 2 REMARK 465 LYS A 3 REMARK 465 THR A 4 REMARK 465 GLU A 178 REMARK 470 REMARK 470 MISSING ATOM REMARK 470 THE FOLLOWING RESIDUES HAVE MISSING ATOMS (M=MODEL NUMBER; REMARK 470 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; REMARK 470 I=INSERTION CODE): REMARK 470 M RES CSSEQI ATOMS REMARK 470 GLU A 93 CG CD OE1 OE2 REMARK 470 ARG A 125 CG CD NE CZ NH1 NH2 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 OD1 ASP A 13 O HOH A 201 2.09 REMARK 500 OE1 GLU A 113 O HOH A 202 2.13 REMARK 500 OD2 ASP A 78 O HOH A 203 2.17 REMARK 500 REMARK 500 REMARK: NULL 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 A 202 O HOH A 220 1454 2.03 REMARK 500 O HOH A 207 O HOH A 271 2656 2.06 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 CYS A 25 -165.61 -124.71 REMARK 500 ASP A 29 106.07 -163.07 REMARK 500 ASP A 78 33.62 -98.29 REMARK 500 SER A 81 -10.03 -142.23 REMARK 500 LYS A 154 -156.79 -112.42 REMARK 500 REMARK 500 REMARK: NULL DBREF 7N3A A 2 178 UNP P22914 CRYGS_HUMAN 2 178 SEQADV 7N3A GLY A 1 UNP P22914 EXPRESSION TAG SEQADV 7N3A ASP A 15 UNP P22914 ASN 15 ENGINEERED MUTATION SEQADV 7N3A GLU A 17 UNP P22914 GLN 17 ENGINEERED MUTATION SEQADV 7N3A ASP A 54 UNP P22914 ASN 54 ENGINEERED MUTATION SEQADV 7N3A GLU A 64 UNP P22914 GLN 64 ENGINEERED MUTATION SEQADV 7N3A GLU A 71 UNP P22914 GLN 71 ENGINEERED MUTATION SEQADV 7N3A GLU A 93 UNP P22914 GLN 93 ENGINEERED MUTATION SEQADV 7N3A GLU A 107 UNP P22914 GLN 107 ENGINEERED MUTATION SEQADV 7N3A GLU A 121 UNP P22914 GLN 121 ENGINEERED MUTATION SEQADV 7N3A ASP A 144 UNP P22914 ASN 144 ENGINEERED MUTATION SEQRES 1 A 178 GLY SER LYS THR GLY THR LYS ILE THR PHE TYR GLU ASP SEQRES 2 A 178 LYS ASP PHE GLU GLY ARG ARG TYR ASP CYS ASP CYS ASP SEQRES 3 A 178 CYS ALA ASP PHE HIS THR TYR LEU SER ARG CYS ASN SER SEQRES 4 A 178 ILE LYS VAL GLU GLY GLY THR TRP ALA VAL TYR GLU ARG SEQRES 5 A 178 PRO ASP PHE ALA GLY TYR MET TYR ILE LEU PRO GLU GLY SEQRES 6 A 178 GLU TYR PRO GLU TYR GLU ARG TRP MET GLY LEU ASN ASP SEQRES 7 A 178 ARG LEU SER SER CYS ARG ALA VAL HIS LEU PRO SER GLY SEQRES 8 A 178 GLY GLU TYR LYS ILE GLN ILE PHE GLU LYS GLY ASP PHE SEQRES 9 A 178 SER GLY GLU MET TYR GLU THR THR GLU ASP CYS PRO SER SEQRES 10 A 178 ILE MET GLU GLU PHE HIS MET ARG GLU ILE HIS SER CYS SEQRES 11 A 178 LYS VAL LEU GLU GLY VAL TRP ILE PHE TYR GLU LEU PRO SEQRES 12 A 178 ASP TYR ARG GLY ARG GLN TYR LEU LEU ASP LYS LYS GLU SEQRES 13 A 178 TYR ARG LYS PRO ILE ASP TRP GLY ALA ALA SER PRO ALA SEQRES 14 A 178 VAL GLN SER PHE ARG ARG ILE VAL GLU FORMUL 2 HOH *110(H2 O) HELIX 1 AA1 ASP A 13 GLU A 17 5 5 HELIX 2 AA2 PRO A 53 PHE A 55 5 3 HELIX 3 AA3 GLU A 69 MET A 74 5 6 HELIX 4 AA4 SER A 117 HIS A 123 1 7 HELIX 5 AA5 LYS A 159 GLY A 164 5 6 SHEET 1 AA1 4 ARG A 20 CYS A 23 0 SHEET 2 AA1 4 LYS A 7 TYR A 11 -1 N PHE A 10 O TYR A 21 SHEET 3 AA1 4 SER A 39 GLU A 43 -1 O GLU A 43 N LYS A 7 SHEET 4 AA1 4 GLY A 65 TYR A 67 -1 O TYR A 67 N ILE A 40 SHEET 1 AA2 3 ALA A 56 LEU A 62 0 SHEET 2 AA2 3 TRP A 47 ARG A 52 -1 N TRP A 47 O LEU A 62 SHEET 3 AA2 3 SER A 82 ALA A 85 -1 O SER A 82 N TYR A 50 SHEET 1 AA3 4 SER A 105 THR A 111 0 SHEET 2 AA3 4 LYS A 95 LYS A 101 -1 N GLU A 100 O GLU A 107 SHEET 3 AA3 4 SER A 129 GLU A 134 -1 O LYS A 131 N GLN A 97 SHEET 4 AA3 4 GLU A 156 TYR A 157 -1 O TYR A 157 N CYS A 130 SHEET 1 AA4 3 ARG A 146 LEU A 152 0 SHEET 2 AA4 3 TRP A 137 LEU A 142 -1 N TRP A 137 O LEU A 152 SHEET 3 AA4 3 SER A 172 ARG A 175 -1 O SER A 172 N TYR A 140 SSBOND 1 CYS A 23 CYS A 27 1555 1555 2.05 CRYST1 29.770 57.710 44.950 90.00 103.33 90.00 P 1 21 1 2 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 0.033591 0.000000 0.007959 0.00000 SCALE2 0.000000 0.017328 0.000000 0.00000 SCALE3 0.000000 0.000000 0.022863 0.00000