PDB Short entry for 4DOU HEADER HORMONE 10-FEB-12 4DOU TITLE CRYSTAL STRUCTURE OF A SINGLE-CHAIN TRIMER OF HUMAN ADIPONECTIN TITLE 2 GLOBULAR DOMAIN COMPND MOL_ID: 1; COMPND 2 MOLECULE: ADIPONECTIN; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: UNP RESIDUES 104-244; COMPND 5 SYNONYM: 30 KDA ADIPOCYTE COMPLEMENT-RELATED PROTEIN,ADIPOCYTE COMPND 6 COMPLEMENT-RELATED 30 KDA PROTEIN,ACRP30,ADIPOCYTE,C1Q AND COLLAGEN COMPND 7 DOMAIN-CONTAINING PROTEIN,ADIPOSE MOST ABUNDANT GENE TRANSCRIPT 1 COMPND 8 PROTEIN,APM-1,GELATIN-BINDING PROTEIN,30 KDA ADIPOCYTE COMPLEMENT- COMPND 9 RELATED PROTEIN, ADIPOCYTE COMPLEMENT-RELATED 30 KDA PROTEIN, ACRP30, COMPND 10 ADIPOCYTE, C1Q AND COLLAGEN DOMAIN-CONTAINING PROTEIN, ADIPOSE MOST COMPND 11 ABUNDANT GENE TRANSCRIPT 1 PROTEIN, APM-1, GELATIN-BINDING PROTEIN; COMPND 12 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 3 ORGANISM_COMMON: HUMAN, HUMAN; SOURCE 4 ORGANISM_TAXID: 9606; SOURCE 5 GENE: ADIPOQ, ACDC, ACRP30, APM1, GBP28, ACDC, ACRP30, ADIPONECTIN, SOURCE 6 ADIPOQ, APM1, GBP28; SOURCE 7 EXPRESSION_SYSTEM: HOMO SAPIENS; SOURCE 8 EXPRESSION_SYSTEM_TAXID: 9606 KEYWDS SINGLE-CHAIN GLOBULAR DOMAIN, CALCIUM BINDING, C1Q-LIKE DOMAIN, KEYWDS 2 GROWTH FACTOR, SERUM, HORMONE EXPDTA X-RAY DIFFRACTION AUTHOR X.MIN,N.P.WALKER,Z.WANG REVDAT 4 13-SEP-23 4DOU 1 REMARK LINK REVDAT 3 31-MAY-17 4DOU 1 COMPND REMARK DBREF REVDAT 2 02-MAY-12 4DOU 1 JRNL REVDAT 1 29-FEB-12 4DOU 0 JRNL AUTH X.MIN,B.LEMON,J.TANG,Q.LIU,R.ZHANG,N.WALKER,Y.LI,Z.WANG JRNL TITL CRYSTAL STRUCTURE OF A SINGLE-CHAIN TRIMER OF HUMAN JRNL TITL 2 ADIPONECTIN GLOBULAR DOMAIN. JRNL REF FEBS LETT. V. 586 912 2012 JRNL REFN ISSN 0014-5793 JRNL PMID 22449980 JRNL DOI 10.1016/J.FEBSLET.2012.02.024 REMARK 2 REMARK 2 RESOLUTION. 2.00 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.5.0066 REMARK 3 AUTHORS : MURSHUDOV,SKUBAK,LEBEDEV,PANNU,STEINER, REMARK 3 : NICHOLLS,WINN,LONG,VAGIN REMARK 3 REMARK 3 REFINEMENT TARGET : MAXIMUM LIKELIHOOD REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.00 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 30.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 91.0 REMARK 3 NUMBER OF REFLECTIONS : 21717 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 CROSS-VALIDATION METHOD : THROUGHOUT REMARK 3 FREE R VALUE TEST SET SELECTION : RANDOM REMARK 3 R VALUE (WORKING + TEST SET) : 0.203 REMARK 3 R VALUE (WORKING SET) : 0.200 REMARK 3 FREE R VALUE : 0.257 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.100 REMARK 3 FREE R VALUE TEST SET COUNT : 1166 REMARK 3 REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN. REMARK 3 TOTAL NUMBER OF BINS USED : 20 REMARK 3 BIN RESOLUTION RANGE HIGH (A) : 2.00 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.05 REMARK 3 REFLECTION IN BIN (WORKING SET) : 1141 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 65.13 REMARK 3 BIN R VALUE (WORKING SET) : 0.2350 REMARK 3 BIN FREE R VALUE SET COUNT : 62 REMARK 3 BIN FREE R VALUE : 0.3030 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 3284 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 30 REMARK 3 SOLVENT ATOMS : 158 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 24.00 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 31.49 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 2.30000 REMARK 3 B22 (A**2) : -1.52000 REMARK 3 B33 (A**2) : -0.82000 REMARK 3 B12 (A**2) : 0.57000 REMARK 3 B13 (A**2) : -0.50000 REMARK 3 B23 (A**2) : -0.16000 REMARK 3 REMARK 3 ESTIMATED OVERALL COORDINATE ERROR. REMARK 3 ESU BASED ON R VALUE (A): 0.281 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.216 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.154 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 11.965 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.947 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.912 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 3413 ; 0.006 ; 0.022 REMARK 3 BOND LENGTHS OTHERS (A): NULL ; NULL ; NULL REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 4617 ; 1.070 ; 1.928 REMARK 3 BOND ANGLES OTHERS (DEGREES): NULL ; NULL ; NULL REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 399 ; 6.027 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 189 ;31.928 ;24.497 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 528 ;15.830 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 9 ;15.282 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 473 ; 0.080 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 2678 ; 0.004 ; 0.020 REMARK 3 GENERAL PLANES OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED CONTACTS OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION OTHERS (A): NULL ; NULL ; NULL REMARK 3 H-BOND (X...Y) REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 H-BOND (X...Y) OTHERS (A): NULL ; NULL ; NULL REMARK 3 POTENTIAL METAL-ION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 POTENTIAL METAL-ION OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY VDW REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY VDW OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY H-BOND REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY H-BOND OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY METAL-ION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY METAL-ION OTHERS (A): NULL ; NULL ; NULL REMARK 3 REMARK 3 ISOTROPIC THERMAL FACTOR RESTRAINTS. COUNT RMS WEIGHT REMARK 3 MAIN-CHAIN BOND REFINED ATOMS (A**2): 1977 ; 0.407 ; 1.500 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 3179 ; 0.729 ; 2.000 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 1436 ; 1.111 ; 3.000 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 1435 ; 1.645 ; 4.500 REMARK 3 SIDE-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 LONG RANGE B REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 LONG RANGE B OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 REMARK 3 ANISOTROPIC THERMAL FACTOR RESTRAINTS. COUNT RMS WEIGHT REMARK 3 RIGID-BOND RESTRAINTS (A**2): NULL ; NULL ; NULL REMARK 3 SPHERICITY; FREE ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SPHERICITY; BONDED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 REMARK 3 NCS RESTRAINTS STATISTICS REMARK 3 NUMBER OF DIFFERENT NCS GROUPS : NULL REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : 3 REMARK 3 REMARK 3 TLS GROUP : 1 REMARK 3 NUMBER OF COMPONENTS GROUP : 3 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : A 108 A 123 REMARK 3 RESIDUE RANGE : A 128 A 216 REMARK 3 RESIDUE RANGE : A 220 A 245 REMARK 3 ORIGIN FOR THE GROUP (A): 9.7507 -20.6857 -5.5564 REMARK 3 T TENSOR REMARK 3 T11: 0.0394 T22: 0.0445 REMARK 3 T33: 0.0617 T12: -0.0150 REMARK 3 T13: 0.0151 T23: 0.0291 REMARK 3 L TENSOR REMARK 3 L11: 1.7102 L22: 3.9721 REMARK 3 L33: 4.5244 L12: -0.4590 REMARK 3 L13: 0.0556 L23: 1.7354 REMARK 3 S TENSOR REMARK 3 S11: -0.0169 S12: 0.2254 S13: 0.1364 REMARK 3 S21: -0.2836 S22: 0.0105 S23: -0.3687 REMARK 3 S31: -0.3862 S32: 0.1709 S33: 0.0064 REMARK 3 REMARK 3 TLS GROUP : 2 REMARK 3 NUMBER OF COMPONENTS GROUP : 2 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : A 246 A 261 REMARK 3 RESIDUE RANGE : A 269 A 386 REMARK 3 ORIGIN FOR THE GROUP (A): -9.3897 -22.5670 1.0321 REMARK 3 T TENSOR REMARK 3 T11: 0.0285 T22: 0.0608 REMARK 3 T33: 0.0948 T12: 0.0247 REMARK 3 T13: 0.0362 T23: 0.0291 REMARK 3 L TENSOR REMARK 3 L11: 1.7725 L22: 4.1892 REMARK 3 L33: 2.7108 L12: 0.8411 REMARK 3 L13: 0.8963 L23: 1.4908 REMARK 3 S TENSOR REMARK 3 S11: 0.0308 S12: -0.0110 S13: 0.0248 REMARK 3 S21: 0.2581 S22: -0.0121 S23: 0.4724 REMARK 3 S31: -0.0625 S32: -0.3519 S33: -0.0187 REMARK 3 REMARK 3 TLS GROUP : 3 REMARK 3 NUMBER OF COMPONENTS GROUP : 2 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : A 391 A 404 REMARK 3 RESIDUE RANGE : A 407 A 525 REMARK 3 ORIGIN FOR THE GROUP (A): 5.8749 -32.4422 11.1525 REMARK 3 T TENSOR REMARK 3 T11: 0.0547 T22: 0.0443 REMARK 3 T33: 0.0226 T12: -0.0043 REMARK 3 T13: -0.0161 T23: 0.0238 REMARK 3 L TENSOR REMARK 3 L11: 1.2857 L22: 4.3020 REMARK 3 L33: 2.5659 L12: -0.3491 REMARK 3 L13: -0.0432 L23: 1.5481 REMARK 3 S TENSOR REMARK 3 S11: 0.0082 S12: -0.1868 S13: -0.0579 REMARK 3 S21: 0.4580 S22: 0.0026 S23: -0.1487 REMARK 3 S31: 0.2194 S32: 0.0984 S33: -0.0109 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : MASK REMARK 3 PARAMETERS FOR MASK CALCULATION REMARK 3 VDW PROBE RADIUS : 1.20 REMARK 3 ION PROBE RADIUS : 0.80 REMARK 3 SHRINKAGE RADIUS : 0.80 REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: HYDROGENS HAVE BEEN ADDED IN THE RIDING REMARK 3 POSITIONS REMARK 4 REMARK 4 4DOU COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 12-FEB-12. REMARK 100 THE DEPOSITION ID IS D_1000070597. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : NULL REMARK 200 TEMPERATURE (KELVIN) : 90 REMARK 200 PH : 5.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : ALS REMARK 200 BEAMLINE : 5.0.2 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.000 REMARK 200 MONOCHROMATOR : DOUBLE-CRYSTAL, SI(111) REMARK 200 OPTICS : MIRRORS REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 315 REMARK 200 INTENSITY-INTEGRATION SOFTWARE : MOSFLM REMARK 200 DATA SCALING SOFTWARE : SCALA REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 72800 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.000 REMARK 200 RESOLUTION RANGE LOW (A) : 43.200 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 2.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 91.0 REMARK 200 DATA REDUNDANCY : 3.200 REMARK 200 R MERGE (I) : 0.06500 REMARK 200 R SYM (I) : NULL REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 10.5000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.00 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.11 REMARK 200 COMPLETENESS FOR SHELL (%) : 72.2 REMARK 200 DATA REDUNDANCY IN SHELL : 3.10 REMARK 200 R MERGE FOR SHELL (I) : 0.32300 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 <I/SIGMA(I)> FOR SHELL : 3.000 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: 1C28 REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 34.72 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 1.88 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 22% PEG3350, 0.1M BIS-TRIS, AND 25% REMARK 280 PEG200, PH 5.5, VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 298K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,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 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 300 REMARK: THE GLOBULAR PROTEIN HAS A TRIMERIC SYMMETRY 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 HIS A 87 REMARK 465 HIS A 88 REMARK 465 HIS A 89 REMARK 465 HIS A 90 REMARK 465 HIS A 91 REMARK 465 HIS A 92 REMARK 465 HIS A 93 REMARK 465 HIS A 94 REMARK 465 GLU A 95 REMARK 465 ASN A 96 REMARK 465 LEU A 97 REMARK 465 TYR A 98 REMARK 465 PHE A 99 REMARK 465 GLN A 100 REMARK 465 GLY A 101 REMARK 465 ALA A 102 REMARK 465 SER A 103 REMARK 465 PRO A 104 REMARK 465 GLY A 105 REMARK 465 GLU A 106 REMARK 465 GLY A 107 REMARK 465 ILE A 125 REMARK 465 PRO A 126 REMARK 465 ASN A 127 REMARK 465 GLY A 217 REMARK 465 GLU A 218 REMARK 465 GLY A 219 REMARK 465 THR A 262 REMARK 465 TYR A 263 REMARK 465 VAL A 264 REMARK 465 THR A 265 REMARK 465 ILE A 266 REMARK 465 PRO A 267 REMARK 465 ASN A 268 REMARK 465 GLY A 387 REMARK 465 GLU A 388 REMARK 465 GLY A 389 REMARK 465 ALA A 390 REMARK 465 VAL A 405 REMARK 465 THR A 406 REMARK 465 ASN A 526 REMARK 465 GLY A 527 REMARK 465 SER A 528 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 THR A 525 OG1 CG2 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 CB GLU A 500 OE2 GLU A 502 1.88 REMARK 500 OE1 GLN A 472 O HOH A 1256 1.99 REMARK 500 O HOH A 1216 O HOH A 1247 2.08 REMARK 500 N GLY A 360 O HOH A 1253 2.08 REMARK 500 N GLU A 359 O HOH A 1253 2.08 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 OE1 GLU A 473 O HOH A 1190 1666 1.73 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: COVALENT BOND LENGTHS REMARK 500 REMARK 500 THE STEREOCHEMICAL PARAMETERS OF THE FOLLOWING RESIDUES REMARK 500 HAVE VALUES WHICH DEVIATE FROM EXPECTED VALUES BY MORE REMARK 500 THAN 6*RMSD (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 500 IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 STANDARD TABLE: REMARK 500 FORMAT: (10X,I3,1X,2(A3,1X,A1,I4,A1,1X,A4,3X),1X,F6.3) REMARK 500 REMARK 500 EXPECTED VALUES PROTEIN: ENGH AND HUBER, 1999 REMARK 500 EXPECTED VALUES NUCLEIC ACID: CLOWNEY ET AL 1996 REMARK 500 REMARK 500 M RES CSSEQI ATM1 RES CSSEQI ATM2 DEVIATION REMARK 500 SER A 146 CB SER A 146 OG 0.097 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 SER A 113 111.56 -161.82 REMARK 500 ASN A 138 44.90 -168.68 REMARK 500 MET A 168 -32.94 84.71 REMARK 500 LYS A 178 56.51 35.99 REMARK 500 ARG A 221 68.68 -109.94 REMARK 500 ASN A 222 40.21 -109.82 REMARK 500 ASP A 227 -149.06 -145.79 REMARK 500 ASP A 229 41.77 -147.53 REMARK 500 LEU A 239 -61.19 -91.23 REMARK 500 ASN A 244 162.24 -21.32 REMARK 500 ASN A 279 43.29 -159.57 REMARK 500 MET A 309 -47.02 80.28 REMARK 500 LYS A 319 -66.57 78.01 REMARK 500 ASP A 320 15.16 -157.56 REMARK 500 ASP A 368 -162.18 -160.63 REMARK 500 ASP A 370 45.93 -140.96 REMARK 500 ASN A 385 -68.88 -94.22 REMARK 500 THR A 403 -139.65 166.66 REMARK 500 ASN A 420 52.43 -161.66 REMARK 500 MET A 450 -29.07 80.51 REMARK 500 ASP A 511 42.45 -148.06 REMARK 500 LEU A 521 -63.74 -95.14 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 CA A1003 CA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP A 187 OD2 REMARK 620 2 GLN A 188 O 84.5 REMARK 620 3 ASP A 195 OD2 91.1 86.7 REMARK 620 4 ASN A 334 OD1 159.3 77.6 98.1 REMARK 620 5 VAL A 335 O 82.5 100.2 170.0 90.4 REMARK 620 6 ASP A 336 OD2 107.5 165.1 84.2 91.9 90.3 REMARK 620 N 1 2 3 4 5 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 CA A1002 CA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASN A 193 OD1 REMARK 620 2 VAL A 194 O 93.3 REMARK 620 3 ASP A 195 OD1 86.2 83.4 REMARK 620 4 ASP A 469 OD1 163.1 72.8 101.2 REMARK 620 5 GLN A 470 O 88.1 104.2 170.8 86.2 REMARK 620 6 ASP A 477 OD2 99.9 159.8 82.2 96.1 91.6 REMARK 620 N 1 2 3 4 5 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 NA A1004 NA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 GLN A 196 O REMARK 620 2 GLN A 337 O 99.9 REMARK 620 3 GLN A 478 O 99.5 98.4 REMARK 620 4 HOH A1113 O 161.9 87.5 95.7 REMARK 620 5 HOH A1136 O 96.7 161.2 87.4 74.1 REMARK 620 6 HOH A1225 O 85.8 96.6 163.0 76.9 75.9 REMARK 620 N 1 2 3 4 5 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 CA A1001 CA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP A 328 OD1 REMARK 620 2 GLN A 329 O 93.3 REMARK 620 3 ASP A 336 OD1 98.8 87.2 REMARK 620 4 ASN A 475 OD1 163.2 78.3 95.3 REMARK 620 5 VAL A 476 O 86.7 105.7 165.7 81.7 REMARK 620 6 ASP A 477 OD1 106.9 159.4 85.6 83.2 80.2 REMARK 620 N 1 2 3 4 5 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CA A 1001 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CA A 1002 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CA A 1003 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE NA A 1004 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE GOL A 1005 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE EDO A 1006 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC7 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE EDO A 1007 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC8 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE EDO A 1009 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC9 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE EDO A 1010 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 1C28 RELATED DB: PDB REMARK 900 MOUSE HOMOLOG REMARK 999 REMARK 999 SEQUENCE REMARK 999 THREE COPIES OF HUMAN ADIPONECTIN GLOBULAR DOMAIN SEQUENCES (PRO104 REMARK 999 TO ASN244) ARE JOINED IN TANDEM DBREF 4DOU A 104 244 UNP Q15848 ADIPO_HUMAN 104 244 DBREF 4DOU A 245 528 PDB 4DOU 4DOU 245 528 SEQADV 4DOU HIS A 87 UNP Q15848 EXPRESSION TAG SEQADV 4DOU HIS A 88 UNP Q15848 EXPRESSION TAG SEQADV 4DOU HIS A 89 UNP Q15848 EXPRESSION TAG SEQADV 4DOU HIS A 90 UNP Q15848 EXPRESSION TAG SEQADV 4DOU HIS A 91 UNP Q15848 EXPRESSION TAG SEQADV 4DOU HIS A 92 UNP Q15848 EXPRESSION TAG SEQADV 4DOU HIS A 93 UNP Q15848 EXPRESSION TAG SEQADV 4DOU HIS A 94 UNP Q15848 EXPRESSION TAG SEQADV 4DOU GLU A 95 UNP Q15848 EXPRESSION TAG SEQADV 4DOU ASN A 96 UNP Q15848 EXPRESSION TAG SEQADV 4DOU LEU A 97 UNP Q15848 EXPRESSION TAG SEQADV 4DOU TYR A 98 UNP Q15848 EXPRESSION TAG SEQADV 4DOU PHE A 99 UNP Q15848 EXPRESSION TAG SEQADV 4DOU GLN A 100 UNP Q15848 EXPRESSION TAG SEQADV 4DOU GLY A 101 UNP Q15848 EXPRESSION TAG SEQADV 4DOU ALA A 102 UNP Q15848 EXPRESSION TAG SEQADV 4DOU SER A 103 UNP Q15848 EXPRESSION TAG SEQRES 1 A 442 HIS HIS HIS HIS HIS HIS HIS HIS GLU ASN LEU TYR PHE SEQRES 2 A 442 GLN GLY ALA SER PRO GLY GLU GLY ALA TYR VAL TYR ARG SEQRES 3 A 442 SER ALA PHE SER VAL GLY LEU GLU THR TYR VAL THR ILE SEQRES 4 A 442 PRO ASN MET PRO ILE ARG PHE THR LYS ILE PHE TYR ASN SEQRES 5 A 442 GLN GLN ASN HIS TYR ASP GLY SER THR GLY LYS PHE HIS SEQRES 6 A 442 CYS ASN ILE PRO GLY LEU TYR TYR PHE ALA TYR HIS ILE SEQRES 7 A 442 THR VAL TYR MET LYS ASP VAL LYS VAL SER LEU PHE LYS SEQRES 8 A 442 LYS ASP LYS ALA MET LEU PHE THR TYR ASP GLN TYR GLN SEQRES 9 A 442 GLU ASN ASN VAL ASP GLN ALA SER GLY SER VAL LEU LEU SEQRES 10 A 442 HIS LEU GLU VAL GLY ASP GLN VAL TRP LEU GLN VAL TYR SEQRES 11 A 442 GLY GLU GLY GLU ARG ASN GLY LEU TYR ALA ASP ASN ASP SEQRES 12 A 442 ASN ASP SER THR PHE THR GLY PHE LEU LEU TYR HIS ASP SEQRES 13 A 442 THR ASN PRO GLY GLU GLY ALA TYR VAL TYR ARG SER ALA SEQRES 14 A 442 PHE SER VAL GLY LEU GLU THR TYR VAL THR ILE PRO ASN SEQRES 15 A 442 MET PRO ILE ARG PHE THR LYS ILE PHE TYR ASN GLN GLN SEQRES 16 A 442 ASN HIS TYR ASP GLY SER THR GLY LYS PHE HIS CYS ASN SEQRES 17 A 442 ILE PRO GLY LEU TYR TYR PHE ALA TYR HIS ILE THR VAL SEQRES 18 A 442 TYR MET LYS ASP VAL LYS VAL SER LEU PHE LYS LYS ASP SEQRES 19 A 442 LYS ALA MET LEU PHE THR TYR ASP GLN TYR GLN GLU ASN SEQRES 20 A 442 ASN VAL ASP GLN ALA SER GLY SER VAL LEU LEU HIS LEU SEQRES 21 A 442 GLU VAL GLY ASP GLN VAL TRP LEU GLN VAL TYR GLY GLU SEQRES 22 A 442 GLY GLU ARG ASN GLY LEU TYR ALA ASP ASN ASP ASN ASP SEQRES 23 A 442 SER THR PHE THR GLY PHE LEU LEU TYR HIS ASP THR ASN SEQRES 24 A 442 PRO GLY GLU GLY ALA TYR VAL TYR ARG SER ALA PHE SER SEQRES 25 A 442 VAL GLY LEU GLU THR TYR VAL THR ILE PRO ASN MET PRO SEQRES 26 A 442 ILE ARG PHE THR LYS ILE PHE TYR ASN GLN GLN ASN HIS SEQRES 27 A 442 TYR ASP GLY SER THR GLY LYS PHE HIS CYS ASN ILE PRO SEQRES 28 A 442 GLY LEU TYR TYR PHE ALA TYR HIS ILE THR VAL TYR MET SEQRES 29 A 442 LYS ASP VAL LYS VAL SER LEU PHE LYS LYS ASP LYS ALA SEQRES 30 A 442 MET LEU PHE THR TYR ASP GLN TYR GLN GLU ASN ASN VAL SEQRES 31 A 442 ASP GLN ALA SER GLY SER VAL LEU LEU HIS LEU GLU VAL SEQRES 32 A 442 GLY ASP GLN VAL TRP LEU GLN VAL TYR GLY GLU GLY GLU SEQRES 33 A 442 ARG ASN GLY LEU TYR ALA ASP ASN ASP ASN ASP SER THR SEQRES 34 A 442 PHE THR GLY PHE LEU LEU TYR HIS ASP THR ASN GLY SER HET CA A1001 1 HET CA A1002 1 HET CA A1003 1 HET NA A1004 1 HET GOL A1005 6 HET EDO A1006 4 HET EDO A1007 4 HET EDO A1008 4 HET EDO A1009 4 HET EDO A1010 4 HETNAM CA CALCIUM ION HETNAM NA SODIUM ION HETNAM GOL GLYCEROL HETNAM EDO 1,2-ETHANEDIOL HETSYN GOL GLYCERIN; PROPANE-1,2,3-TRIOL HETSYN EDO ETHYLENE GLYCOL FORMUL 2 CA 3(CA 2+) FORMUL 5 NA NA 1+ FORMUL 6 GOL C3 H8 O3 FORMUL 7 EDO 5(C2 H6 O2) FORMUL 12 HOH *158(H2 O) LINK OD2 ASP A 187 CA CA A1003 1555 1555 2.36 LINK O GLN A 188 CA CA A1003 1555 1555 2.47 LINK OD1 ASN A 193 CA CA A1002 1555 1555 2.62 LINK O VAL A 194 CA CA A1002 1555 1555 2.27 LINK OD1 ASP A 195 CA CA A1002 1555 1555 2.46 LINK OD2 ASP A 195 CA CA A1003 1555 1555 2.29 LINK O GLN A 196 NA NA A1004 1555 1555 2.38 LINK OD1 ASP A 328 CA CA A1001 1555 1555 2.32 LINK O GLN A 329 CA CA A1001 1555 1555 2.38 LINK OD1 ASN A 334 CA CA A1003 1555 1555 2.46 LINK O VAL A 335 CA CA A1003 1555 1555 2.32 LINK OD1 ASP A 336 CA CA A1001 1555 1555 2.35 LINK OD2 ASP A 336 CA CA A1003 1555 1555 2.23 LINK O GLN A 337 NA NA A1004 1555 1555 2.41 LINK OD1 ASP A 469 CA CA A1002 1555 1555 2.33 LINK O GLN A 470 CA CA A1002 1555 1555 2.45 LINK OD1 ASN A 475 CA CA A1001 1555 1555 2.45 LINK O VAL A 476 CA CA A1001 1555 1555 2.31 LINK OD1 ASP A 477 CA CA A1001 1555 1555 2.44 LINK OD2 ASP A 477 CA CA A1002 1555 1555 2.23 LINK O GLN A 478 NA NA A1004 1555 1555 2.38 LINK NA NA A1004 O HOH A1113 1555 1555 2.52 LINK NA NA A1004 O HOH A1136 1555 1555 2.45 LINK NA NA A1004 O HOH A1225 1555 1555 2.63 CISPEP 1 PRO A 245 GLY A 246 0 -5.72 SITE 1 AC1 6 ASP A 328 GLN A 329 ASP A 336 ASN A 475 SITE 2 AC1 6 VAL A 476 ASP A 477 SITE 1 AC2 6 ASN A 193 VAL A 194 ASP A 195 ASP A 469 SITE 2 AC2 6 GLN A 470 ASP A 477 SITE 1 AC3 6 ASP A 187 GLN A 188 ASP A 195 ASN A 334 SITE 2 AC3 6 VAL A 335 ASP A 336 SITE 1 AC4 6 GLN A 196 GLN A 337 GLN A 478 HOH A1113 SITE 2 AC4 6 HOH A1136 HOH A1225 SITE 1 AC5 2 PRO A 411 LYS A 431 SITE 1 AC6 6 TYR A 381 TYR A 393 LEU A 521 TYR A 522 SITE 2 AC6 6 HIS A 523 HOH A1251 SITE 1 AC7 5 LYS A 177 LEU A 203 HIS A 204 PHE A 277 SITE 2 AC7 5 HOH A1232 SITE 1 AC8 2 TYR A 449 VAL A 476 SITE 1 AC9 2 VAL A 215 TYR A 216 CRYST1 48.310 49.630 50.460 117.23 101.68 105.31 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 0.020700 0.005667 0.008734 0.00000 SCALE2 0.000000 0.020891 0.013439 0.00000 SCALE3 0.000000 0.000000 0.024062 0.00000