HEADER STRUCTURAL PROTEIN 06-JUL-09 2KLJ TITLE SOLUTION STRUCTURE OF GAMMAD-CRYSTALLIN WITH RDC AND SAXS 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 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_VECTOR: PQE.1 KEYWDS GAMMAD-CRYSTALLIN, 3D STRUCTURE, RDC, SAXS, CATARACT, DISEASE KEYWDS 2 MUTATION, EYE LENS PROTEIN, OXIDATION, POLYMORPHISM, SENSORY KEYWDS 3 TRANSDUCTION, VISION, STRUCTURAL PROTEIN EXPDTA SOLUTION SCATTERING; SOLUTION NMR NUMMDL 10 AUTHOR J.WANG,X.ZUO,P.YU,I.BYEON,J.JUNG,A.M.GRONENBORN,Y.WANG REVDAT 3 16-MAR-22 2KLJ 1 REMARK SEQADV REVDAT 2 07-APR-10 2KLJ 1 REMARK REVDAT 1 06-OCT-09 2KLJ 0 JRNL AUTH J.WANG,X.ZUO,P.YU,I.J.BYEON,J.JUNG,X.WANG,M.DYBA,S.SEIFERT, JRNL AUTH 2 C.D.SCHWIETERS,J.QIN,A.M.GRONENBORN,Y.X.WANG JRNL TITL DETERMINATION OF MULTICOMPONENT PROTEIN STRUCTURES IN JRNL TITL 2 SOLUTION USING GLOBAL ORIENTATION AND SHAPE RESTRAINTS. JRNL REF J.AM.CHEM.SOC. V. 131 10507 2009 JRNL REFN ISSN 0002-7863 JRNL PMID 19722627 JRNL DOI 10.1021/JA902528F REMARK 1 REMARK 1 REFERENCE 1 REMARK 1 AUTH J.JUNG,I.L.BYEON,Y.WANG,J.KING,A.M.GRONENBORN REMARK 1 TITL THE STRUCTURE OF THE CATARACT-CAUSING P23T MUTANT OF HGD REMARK 1 TITL 2 CRYSTALLIN EXHIBITS DISTINCTIVE LOCAL CONFORMATIONAL AND REMARK 1 TITL 3 DYNAMIC CHANGES REMARK 1 REF BIOCHEMISTRY V. 48 2597 2009 REMARK 1 REFN ISSN 0006-2960 REMARK 1 PMID 19216553 REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : X-PLOR NIH 2.22 REMARK 3 AUTHORS : SCHWIETERS, KUSZEWSKI, TJANDRA AND CLORE REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 2KLJ COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 23-JUL-09. REMARK 100 THE DEPOSITION ID IS D_1000101270. 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 : 0.02 REMARK 210 PRESSURE : AMBIENT REMARK 210 SAMPLE CONTENTS : 0.2 MM ENTITY-1, 95% H2O/5% D2O; REMARK 210 0.8 MM [U-100% 15N] ENTITY-2, 95% REMARK 210 H2O/5% D2O REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : 2D 1H-15N HSQC REMARK 210 SPECTROMETER FIELD STRENGTH : 900 MHZ REMARK 210 SPECTROMETER MODEL : AVANCE REMARK 210 SPECTROMETER MANUFACTURER : BRUKER REMARK 210 REMARK 210 STRUCTURE DETERMINATION. REMARK 210 SOFTWARE USED : NULL REMARK 210 METHOD USED : SIMULATED ANNEALING REMARK 210 REMARK 210 CONFORMERS, NUMBER CALCULATED : 100 REMARK 210 CONFORMERS, NUMBER SUBMITTED : 10 REMARK 210 CONFORMERS, SELECTION CRITERIA : STRUCTURES WITH THE LOWEST REMARK 210 ENERGY 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 265 REMARK 265 EXPERIMENTAL DETAILS REMARK 265 REMARK 265 EXPERIMENT TYPE : SMALL ANGLE X-RAY SCATTERING REMARK 265 DATA ACQUISITION REMARK 265 RADIATION/NEUTRON SOURCE : APS ARGONNE REMARK 265 SYNCHROTRON (Y/N) : Y REMARK 265 BEAMLINE TYPE : 12-ID REMARK 265 BEAMLINE INSTRUMENT : NULL REMARK 265 DETECTOR TYPE : CCD CAMERA REMARK 265 DETECTOR MANUFACTURER DETAILS : HOME-MADE REMARK 265 TEMPERATURE (KELVIN) : 298 REMARK 265 PH : 6.2 REMARK 265 NUMBER OF TIME FRAMES USED : 20 REMARK 265 PROTEIN CONCENTRATION RANGE (MG/ML) : 1.0-3.6 REMARK 265 SAMPLE BUFFER : 20 MM NACL 20 MM MES REMARK 265 5 MM DTT REMARK 265 DATA REDUCTION SOFTWARE : MARDETECTOR, HOME- REMARK 265 WRITTEN PROGRAM REMARK 265 GUINIER MEAN RADIUS OF GYRATION (NM) : 1.72 REMARK 265 SIGMA MEAN RADIUS OF GYRATION : 0.03 REMARK 265 R(XS-1) MEAN CROSS SECTIONAL RADII (NM) : NULL REMARK 265 R(XS-1) SIGMA MEAN CROSS SECTIONAL RADII : NULL REMARK 265 R(XS-2) MEAN CROSS SECTIONAL RADII (NM) : NULL REMARK 265 R(XS-2) SIGMA MEAN CROSS SECTIONAL RADII : NULL REMARK 265 P(R) PROTEIN LENGTH (NM) : 0.5 REMARK 265 REMARK 265 DATA ANALYSIS AND MODEL FITTING: REMARK 265 METHOD USED TO DETERMINE THE STRUCTURE: NULL REMARK 265 SOFTWARE USED : GNOM REMARK 265 SOFTWARE AUTHORS : NULL REMARK 265 STARTING MODEL : NULL REMARK 265 REMARK 265 CONFORMERS, NUMBER CALCULATED : 100 REMARK 265 CONFORMERS, NUMBER SUBMITTED : 10 REMARK 265 CONFORMERS, SELECTION CRITERIA : STRUCTURES WITH THE LOWEST REMARK 265 ENERGY REMARK 265 REMARK 265 BEST REPRESENTATIVE CONFORMER IN THIS ENSEMBLE : 1 REMARK 265 REMARK 265 OTHER DETAILS: 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: 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 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 H LEU A 26 O ARG A 77 1.56 REMARK 500 O LEU A 112 H ARG A 115 1.57 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 97.76 -173.84 REMARK 500 1 ARG A 10 -176.57 -55.42 REMARK 500 1 GLN A 13 -168.37 -110.83 REMARK 500 1 PRO A 28 6.27 -61.04 REMARK 500 1 TYR A 29 -36.45 -137.85 REMARK 500 1 ARG A 32 -36.08 -142.37 REMARK 500 1 CYS A 33 73.92 69.80 REMARK 500 1 SER A 40 100.73 -172.50 REMARK 500 1 TYR A 51 73.82 42.87 REMARK 500 1 ARG A 60 116.51 -26.62 REMARK 500 1 HIS A 84 -152.88 -105.46 REMARK 500 1 SER A 85 131.45 172.99 REMARK 500 1 GLU A 94 -70.41 -57.38 REMARK 500 1 ASP A 97 -115.30 64.42 REMARK 500 1 TYR A 98 46.92 -158.14 REMARK 500 1 CYS A 111 73.32 -164.66 REMARK 500 1 GLN A 113 -12.62 -46.24 REMARK 500 1 ARG A 117 -80.83 -73.33 REMARK 500 1 SER A 123 138.11 156.33 REMARK 500 1 GLU A 128 -138.16 -80.83 REMARK 500 1 TYR A 139 71.99 44.92 REMARK 500 1 ARG A 163 106.97 -40.94 REMARK 500 1 ASP A 172 16.04 -148.88 REMARK 500 1 PHE A 173 -78.70 -141.40 REMARK 500 2 LYS A 3 97.45 176.34 REMARK 500 2 GLN A 13 -153.97 -129.43 REMARK 500 2 PRO A 28 14.81 -66.30 REMARK 500 2 TYR A 29 -47.64 -136.02 REMARK 500 2 ARG A 32 -37.53 -130.69 REMARK 500 2 SER A 35 143.25 176.49 REMARK 500 2 SER A 40 101.35 -175.33 REMARK 500 2 TYR A 51 79.58 53.08 REMARK 500 2 ARG A 60 107.91 -29.59 REMARK 500 2 ASP A 74 32.51 -94.74 REMARK 500 2 SER A 85 139.00 -179.10 REMARK 500 2 ASP A 97 -113.24 64.83 REMARK 500 2 TYR A 98 47.53 -162.42 REMARK 500 2 GLN A 113 -10.16 -47.31 REMARK 500 2 ARG A 117 -80.05 -65.92 REMARK 500 2 SER A 123 144.47 158.81 REMARK 500 2 ASN A 138 7.08 49.60 REMARK 500 2 TYR A 139 71.18 57.58 REMARK 500 2 ARG A 140 45.00 -143.34 REMARK 500 2 PRO A 148 108.20 -51.62 REMARK 500 2 ARG A 163 121.19 -23.78 REMARK 500 2 VAL A 170 47.66 -83.17 REMARK 500 2 ASP A 172 35.45 -166.32 REMARK 500 2 PHE A 173 -67.38 -137.88 REMARK 500 3 LYS A 3 97.86 -172.21 REMARK 500 3 ARG A 32 -37.55 -136.93 REMARK 500 REMARK 500 THIS ENTRY HAS 225 RAMACHANDRAN OUTLIERS. REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 2KFB RELATED DB: PDB DBREF 2KLJ A 2 174 UNP P07320 CRGD_HUMAN 2 174 SEQADV 2KLJ GLN A 1 UNP P07320 EXPRESSION TAG SEQADV 2KLJ THR A 24 UNP P07320 PRO 24 VARIANT SEQRES 1 A 174 GLN GLY LYS ILE THR LEU TYR GLU ASP ARG GLY PHE GLN SEQRES 2 A 174 GLY ARG HIS TYR GLU CYS SER SER ASP HIS THR ASN LEU SEQRES 3 A 174 GLN PRO TYR LEU SER ARG CYS ASN SER ALA ARG VAL ASP SEQRES 4 A 174 SER GLY CYS TRP MET LEU TYR GLU GLN PRO ASN TYR SER SEQRES 5 A 174 GLY LEU GLN TYR PHE LEU ARG ARG GLY ASP TYR ALA ASP SEQRES 6 A 174 HIS GLN GLN TRP MET GLY LEU SER ASP SER VAL ARG SER SEQRES 7 A 174 CYS ARG LEU ILE PRO HIS SER GLY SER HIS ARG ILE ARG SEQRES 8 A 174 LEU TYR GLU ARG GLU ASP TYR ARG GLY GLN MET ILE GLU SEQRES 9 A 174 PHE THR GLU ASP CYS SER CYS LEU GLN ASP ARG PHE ARG SEQRES 10 A 174 PHE ASN GLU ILE HIS SER LEU ASN VAL LEU GLU GLY SER SEQRES 11 A 174 TRP VAL LEU TYR GLU LEU SER ASN TYR ARG GLY ARG GLN SEQRES 12 A 174 TYR LEU LEU MET PRO GLY ASP TYR ARG ARG TYR GLN ASP SEQRES 13 A 174 TRP GLY ALA THR ASN ALA ARG VAL GLY SER LEU ARG ARG SEQRES 14 A 174 VAL ILE ASP PHE SER HELIX 1 1 HIS A 66 MET A 70 5 5 HELIX 2 2 CYS A 111 ARG A 115 5 5 HELIX 3 3 TYR A 154 GLY A 158 5 5 SHEET 1 A 4 GLN A 13 CYS A 19 0 SHEET 2 A 4 ILE A 4 ASP A 9 -1 N GLU A 8 O ARG A 15 SHEET 3 A 4 SER A 35 TYR A 46 -1 O SER A 35 N TYR A 7 SHEET 4 A 4 GLN A 55 TYR A 63 -1 O LEU A 58 N TRP A 43 SHEET 1 B 4 GLN A 13 CYS A 19 0 SHEET 2 B 4 ILE A 4 ASP A 9 -1 N GLU A 8 O ARG A 15 SHEET 3 B 4 SER A 35 TYR A 46 -1 O SER A 35 N TYR A 7 SHEET 4 B 4 SER A 78 ILE A 82 -1 O SER A 78 N TYR A 46 SHEET 1 C 4 MET A 102 PHE A 105 0 SHEET 2 C 4 ILE A 90 TYR A 93 -1 N ILE A 90 O PHE A 105 SHEET 3 C 4 LEU A 124 VAL A 126 -1 O ASN A 125 N ARG A 91 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 LEU A 133 O TYR A 144 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 MODEL 1