PDB Short entry for 2KFB HEADER STRUCTURAL PROTEIN 12-FEB-09 2KFB TITLE THE STRUCTURE OF THE CATARACT CAUSING P23T MUTANT OF HUMAN GAMMA-D TITLE 2 CRYSTALLIN COMPND MOL_ID: 1; COMPND 2 MOLECULE: GAMMA-CRYSTALLIN D; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: GAMMA-D-CRYSTALLIN, GAMMA-CRYSTALLIN 4; 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: CRYGD, CRYG4; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 8 EXPRESSION_SYSTEM_STRAIN: BL21; SOURCE 9 EXPRESSION_SYSTEM_VARIANT: (DE3); SOURCE 10 EXPRESSION_SYSTEM_VECTOR: PET16B; SOURCE 11 OTHER_DETAILS: ROSETTA 2 KEYWDS CRYSTALLIN, CATARACT, PROTEIN, LENS, DISEASE MUTATION, EYE LENS KEYWDS 2 PROTEIN, OXIDATION, SENSORY TRANSDUCTION, VISION, STRUCTURAL PROTEIN EXPDTA SOLUTION NMR NUMMDL 20 AUTHOR J.JUNG,I.L.BYEON,Y.WANG,J.KING,A.M.GRONENBORN REVDAT 3 20-OCT-21 2KFB 1 REMARK SEQADV REVDAT 2 19-JUN-13 2KFB 1 JRNL VERSN REVDAT 1 28-JUL-09 2KFB 0 JRNL AUTH J.JUNG,I.J.BYEON,Y.WANG,J.KING,A.M.GRONENBORN JRNL TITL THE STRUCTURE OF THE CATARACT-CAUSING P23T MUTANT OF HUMAN JRNL TITL 2 GAMMAD-CRYSTALLIN EXHIBITS DISTINCTIVE LOCAL CONFORMATIONAL JRNL TITL 3 AND DYNAMIC CHANGES. JRNL REF BIOCHEMISTRY V. 48 2597 2009 JRNL REFN ISSN 0006-2960 JRNL PMID 19216553 JRNL DOI 10.1021/BI802292Q REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : CNS, X-PLOR NIH REMARK 3 AUTHORS : BRUNGER A. T. ET.AL. (CNS), SCHWIETERS, KUSZEWSKI, REMARK 3 TJANDRA AND CLORE (X-PLOR NIH) REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 2KFB COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 18-FEB-09. REMARK 100 THE DEPOSITION ID IS D_1000101050. REMARK 210 REMARK 210 EXPERIMENTAL DETAILS REMARK 210 EXPERIMENT TYPE : NMR REMARK 210 TEMPERATURE (KELVIN) : 298 REMARK 210 PH : 6.2 REMARK 210 IONIC STRENGTH : 0.025333 REMARK 210 PRESSURE : AMBIENT REMARK 210 SAMPLE CONTENTS : 0.2-0.8 MM [U-99% 13C; U-99% REMARK 210 15N] P23T, 20 MM SODIUM REMARK 210 PHOSPHATE, 5 MM DTT, 5 % [U-2H] REMARK 210 D2O, 95% H2O/5% D2O; 0.2-0.8 MM REMARK 210 [U-99% 13C; U-99% 15N] P23T, 20 REMARK 210 MM SODIUM PHOSPHATE, 5 MM DTT, 5 REMARK 210 % [U-2H] D2O, 5 % PENTAETHYLENE REMARK 210 GLYCOL MONODODECYL ETHER, 5.2 % REMARK 210 HEXANOL, 95% H2O/5% D2O REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : 3D HNCACB; 3D CBCA(CO)NH; 3D REMARK 210 HCCH-TOCSY; 3D HBHA(CO)NH; 3D 1H- REMARK 210 15N NOESY; 3D 1H-13C NOESY; 2D REMARK 210 1H-15N HSQC REMARK 210 SPECTROMETER FIELD STRENGTH : 600 MHZ; 700 MHZ; 800 MHZ REMARK 210 SPECTROMETER MODEL : AVANCE REMARK 210 SPECTROMETER MANUFACTURER : BRUKER REMARK 210 REMARK 210 STRUCTURE DETERMINATION. REMARK 210 SOFTWARE USED : CYANA, SPARKY REMARK 210 METHOD USED : TORSION ANGLE DYNAMICS, REMARK 210 SIMULATED ANNEALING REMARK 210 REMARK 210 CONFORMERS, NUMBER CALCULATED : 100 REMARK 210 CONFORMERS, NUMBER SUBMITTED : 20 REMARK 210 CONFORMERS, SELECTION CRITERIA : TARGET FUNCTION REMARK 210 REMARK 210 BEST REPRESENTATIVE CONFORMER IN THIS ENSEMBLE : 1 REMARK 210 REMARK 210 REMARK: NULL REMARK 215 REMARK 215 NMR STUDY REMARK 215 THE COORDINATES IN THIS ENTRY WERE GENERATED FROM SOLUTION REMARK 215 NMR DATA. PROTEIN DATA BANK CONVENTIONS REQUIRE THAT REMARK 215 CRYST1 AND SCALE RECORDS BE INCLUDED, BUT THE VALUES ON REMARK 215 THESE RECORDS ARE MEANINGLESS. 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: 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. (RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 465 SSSEQ=SEQUENCE NUMBER; I=INSERTION CODE.) REMARK 465 MODELS 1-20 REMARK 465 RES C SSSEQI REMARK 465 MET A -7 REMARK 465 LYS A -6 REMARK 465 HIS A -5 REMARK 465 HIS A -4 REMARK 465 HIS A -3 REMARK 465 HIS A -2 REMARK 465 HIS A -1 REMARK 465 HIS A 0 REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CLOSE CONTACTS 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 O LEU A 26 H LEU A 30 1.58 REMARK 500 O ARG A 32 O SER A 75 2.11 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 1 LYS A 3 107.63 -167.66 REMARK 500 1 ARG A 10 -173.78 -63.76 REMARK 500 1 PHE A 12 70.41 50.29 REMARK 500 1 GLN A 13 -159.63 -133.69 REMARK 500 1 ARG A 32 -70.82 -145.00 REMARK 500 1 CYS A 33 71.68 76.69 REMARK 500 1 ARG A 60 124.73 -38.49 REMARK 500 1 GLN A 67 -9.86 -49.50 REMARK 500 1 MET A 70 19.16 80.52 REMARK 500 1 ASP A 74 -172.48 -55.57 REMARK 500 1 SER A 75 -122.91 99.25 REMARK 500 1 VAL A 76 102.27 89.65 REMARK 500 1 HIS A 84 131.14 80.92 REMARK 500 1 SER A 85 -1.51 -160.65 REMARK 500 1 THR A 106 25.98 -143.07 REMARK 500 1 GLU A 107 -166.86 -166.50 REMARK 500 1 GLN A 113 -9.28 -47.73 REMARK 500 1 SER A 123 150.96 167.44 REMARK 500 1 SER A 130 151.66 -32.28 REMARK 500 1 TYR A 139 78.81 35.48 REMARK 500 1 ARG A 140 45.60 -149.01 REMARK 500 1 ASN A 161 -165.49 -172.00 REMARK 500 1 ARG A 163 116.77 -31.90 REMARK 500 2 LYS A 3 103.31 -172.81 REMARK 500 2 ARG A 10 -176.22 -59.58 REMARK 500 2 GLN A 13 -155.66 -129.92 REMARK 500 2 ARG A 32 -58.04 -147.50 REMARK 500 2 CYS A 33 74.83 63.08 REMARK 500 2 ARG A 60 127.32 -34.02 REMARK 500 2 GLN A 67 -8.94 -51.98 REMARK 500 2 MET A 70 30.55 72.55 REMARK 500 2 LEU A 72 -52.61 -6.53 REMARK 500 2 ASP A 74 40.51 -67.17 REMARK 500 2 ASP A 97 23.68 39.89 REMARK 500 2 TYR A 98 75.91 35.40 REMARK 500 2 THR A 106 31.57 -143.66 REMARK 500 2 GLU A 107 -169.08 -170.85 REMARK 500 2 GLN A 113 -14.01 -42.75 REMARK 500 2 ARG A 115 -39.13 -132.16 REMARK 500 2 PHE A 118 146.84 -37.29 REMARK 500 2 SER A 123 151.46 165.21 REMARK 500 2 SER A 130 148.38 -31.60 REMARK 500 2 TYR A 139 77.86 39.24 REMARK 500 2 ARG A 140 41.18 -146.57 REMARK 500 2 LEU A 167 145.06 -173.57 REMARK 500 2 PHE A 173 -79.89 -59.54 REMARK 500 3 LYS A 3 106.74 -171.88 REMARK 500 3 ARG A 10 -174.48 -59.84 REMARK 500 3 GLN A 13 -160.83 -128.15 REMARK 500 3 ARG A 32 120.58 177.59 REMARK 500 REMARK 500 THIS ENTRY HAS 485 RAMACHANDRAN OUTLIERS. REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 16173 RELATED DB: BMRB DBREF 2KFB A 2 174 UNP P07320 CRGD_HUMAN 2 174 SEQADV 2KFB MET A -7 UNP P07320 EXPRESSION TAG SEQADV 2KFB LYS A -6 UNP P07320 EXPRESSION TAG SEQADV 2KFB HIS A -5 UNP P07320 EXPRESSION TAG SEQADV 2KFB HIS A -4 UNP P07320 EXPRESSION TAG SEQADV 2KFB HIS A -3 UNP P07320 EXPRESSION TAG SEQADV 2KFB HIS A -2 UNP P07320 EXPRESSION TAG SEQADV 2KFB HIS A -1 UNP P07320 EXPRESSION TAG SEQADV 2KFB HIS A 0 UNP P07320 EXPRESSION TAG SEQADV 2KFB GLN A 1 UNP P07320 EXPRESSION TAG SEQADV 2KFB THR A 24 UNP P07320 PRO 24 ENGINEERED MUTATION SEQRES 1 A 182 MET LYS HIS HIS HIS HIS HIS HIS GLN GLY LYS ILE THR SEQRES 2 A 182 LEU TYR GLU ASP ARG GLY PHE GLN GLY ARG HIS TYR GLU SEQRES 3 A 182 CYS SER SER ASP HIS THR ASN LEU GLN PRO TYR LEU SER SEQRES 4 A 182 ARG CYS ASN SER ALA ARG VAL ASP SER GLY CYS TRP MET SEQRES 5 A 182 LEU TYR GLU GLN PRO ASN TYR SER GLY LEU GLN TYR PHE SEQRES 6 A 182 LEU ARG ARG GLY ASP TYR ALA ASP HIS GLN GLN TRP MET SEQRES 7 A 182 GLY LEU SER ASP SER VAL ARG SER CYS ARG LEU ILE PRO SEQRES 8 A 182 HIS SER GLY SER HIS ARG ILE ARG LEU TYR GLU ARG GLU SEQRES 9 A 182 ASP TYR ARG GLY GLN MET ILE GLU PHE THR GLU ASP CYS SEQRES 10 A 182 SER CYS LEU GLN ASP ARG PHE ARG PHE ASN GLU ILE HIS SEQRES 11 A 182 SER LEU ASN VAL LEU GLU GLY SER TRP VAL LEU TYR GLU SEQRES 12 A 182 LEU SER ASN TYR ARG GLY ARG GLN TYR LEU LEU MET PRO SEQRES 13 A 182 GLY ASP TYR ARG ARG TYR GLN ASP TRP GLY ALA THR ASN SEQRES 14 A 182 ALA ARG VAL GLY SER LEU ARG ARG VAL ILE ASP PHE SER HELIX 1 1 ASP A 65 MET A 70 5 6 HELIX 2 2 CYS A 111 ARG A 115 5 5 HELIX 3 3 ARG A 153 GLY A 158 5 6 SHEET 1 A 4 GLN A 13 CYS A 19 0 SHEET 2 A 4 LYS A 3 ASP A 9 -1 N LEU A 6 O TYR A 17 SHEET 3 A 4 SER A 35 SER A 40 -1 O ARG A 37 N THR A 5 SHEET 4 A 4 GLY A 61 TYR A 63 -1 O TYR A 63 N ALA A 36 SHEET 1 B 3 GLN A 55 LEU A 58 0 SHEET 2 B 3 CYS A 42 TYR A 46 -1 N TRP A 43 O LEU A 58 SHEET 3 B 3 SER A 78 ILE A 82 -1 O ARG A 80 N MET A 44 SHEET 1 C 4 ARG A 99 PHE A 105 0 SHEET 2 C 4 ARG A 89 ARG A 95 -1 N GLU A 94 O GLN A 101 SHEET 3 C 4 SER A 123 GLU A 128 -1 O SER A 123 N TYR A 93 SHEET 4 C 4 GLY A 149 TYR A 151 -1 O TYR A 151 N LEU A 124 SHEET 1 D 3 GLN A 143 LEU A 146 0 SHEET 2 D 3 TRP A 131 TYR A 134 -1 N TRP A 131 O LEU A 146 SHEET 3 D 3 SER A 166 ARG A 169 -1 O SER A 166 N TYR A 134 CRYST1 1.000 1.000 1.000 90.00 90.00 90.00 P 1 1 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 1.000000 0.000000 0.000000 0.00000 SCALE2 0.000000 1.000000 0.000000 0.00000 SCALE3 0.000000 0.000000 1.000000 0.00000